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Cabrera-Sosa L, Safarpour M, Kattenberg JH, Ramirez R, Vinetz J, Rosanas-Urgell A, Gamboa D, Delgado-Ratto C. Comparing newly developed SNP barcode panels with microsatellites to explore population genetics of malaria parasites in the Peruvian Amazon. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.09.611954. [PMID: 39314390 PMCID: PMC11418992 DOI: 10.1101/2024.09.09.611954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Malaria molecular surveillance (MMS) can provide insights into transmission dynamics, guiding national control/elimination programs. Considering the genetic differences among parasites from different areas in the Peruvian Amazon, we previously designed SNP barcode panels for Plasmodium vivax (Pv) and P. falciparum (Pf), integrated into AmpliSeq assays, to provide population genetics estimates of malaria parasites. These AmpliSeq assays are ideal for MMS: multiplexing different traits of interest, applicable to many use cases, and high throughput for large numbers of samples. The present study compares the genetic resolution of the SNP barcode panels in the AmpliSeq assays with widely used microsatellite (MS) panels to investigate Amazonian malaria parasites. Malaria samples collected in remote areas of the Peruvian Amazon (51 Pv & 80 Pf samples) were characterized using the Ampliseq assays and MS. Population genetics estimates (complexity of infection, genetic diversity and differentiation, and population structure) were compared using the SNP barcodes (Pv: 40 SNPs & Pf: 28 SNPs) and MS panels (Pv: 16 MS & Pf: 7 MS). The genetic diversity of Pv (expected heterozygosity, He ) was similar across the subpopulations for both makers: He MS = 0.68 - 0.78 (p = 0.23) and He SNP = 0.36 - 0.38 (p = 0.80). Pairwise genetic differentiation (fixation index, F ST ) was also comparable: F ST-MS = 0.04 - 0.14 and F ST-SNP = 0.03 - 0.12 (p = 0.34 - 0.85). No geographic clustering was observed with any panel. In addition, Pf genetic diversity trends ( He MS = 0 - 0.48 p = 0.03 - 1; He SNP = 0 - 0.09, p = 0.03 - 1) and pairwise F ST comparisons (F ST-MS = 0.14 - 0.65, F ST-SNP = 0.19 - 0.61, p = 0.24 - 0.83) were concordant between the panels. Similar population structure clustering was observed with both SNP and MS, highlighting one Pf subpopulation in an indigenous community. The SNP barcodes in the Pv AmpliSeq v2 Peru and Pf AmpliSeq v1 Peru assays offer comparable results to MS panels when investigating population genetics in Pv and Pv populations. Therefore, the AmpliSeq assays can efficiently characterize malaria transmission dynamics and population structure and support malaria elimination efforts in Peru.
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Siegel SV, Trimarsanto H, Amato R, Murie K, Taylor AR, Sutanto E, Kleinecke M, Whitton G, Watson JA, Imwong M, Assefa A, Rahim AG, Nguyen HC, Tran TH, Green JA, Koh GCKW, White NJ, Day N, Kwiatkowski DP, Rayner JC, Price RN, Auburn S. Lineage-informative microhaplotypes for recurrence classification and spatio-temporal surveillance of Plasmodium vivax malaria parasites. Nat Commun 2024; 15:6757. [PMID: 39117628 PMCID: PMC11310204 DOI: 10.1038/s41467-024-51015-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/25/2024] [Indexed: 08/10/2024] Open
Abstract
Challenges in classifying recurrent Plasmodium vivax infections constrain surveillance of antimalarial efficacy and transmission. Recurrent infections may arise from activation of dormant liver stages (relapse), blood-stage treatment failure (recrudescence) or reinfection. Molecular inference of familial relatedness (identity-by-descent or IBD) can help resolve the probable origin of recurrences. As whole genome sequencing of P. vivax remains challenging, targeted genotyping methods are needed for scalability. We describe a P. vivax marker discovery framework to identify and select panels of microhaplotypes (multi-allelic markers within small, amplifiable segments of the genome) that can accurately capture IBD. We evaluate panels of 50-250 microhaplotypes discovered in a global set of 615 P. vivax genomes. A candidate global 100-microhaplotype panel exhibits high marker diversity in the Asia-Pacific, Latin America and horn of Africa (median HE = 0.70-0.81) and identifies 89% of the polyclonal infections detected with genome-wide datasets. Data simulations reveal lower error in estimating pairwise IBD using microhaplotypes relative to traditional biallelic SNP barcodes. The candidate global panel also exhibits high accuracy in predicting geographic origin and captures local infection outbreak and bottlenecking events. Our framework is open-source enabling customised microhaplotype discovery and selection, with potential for porting to other species or data resources.
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Affiliation(s)
- Sasha V Siegel
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, 0811, Australia
| | - Hidayat Trimarsanto
- Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, 0811, Australia
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Jakarta, 10430, Indonesia
| | - Roberto Amato
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Kathryn Murie
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Aimee R Taylor
- Institut Pasteur, University de Paris, Infectious Disease Epidemiology and Analytics Unit, Paris, France
| | - Edwin Sutanto
- Exeins Health Initiative, Jakarta Selatan, 12870, Indonesia
| | - Mariana Kleinecke
- Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, 0811, Australia
| | | | - James A Watson
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7LJ, UK
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, 764 Vo Van Kiet, W.1, Dist.5, Ho Chi Minh City, Vietnam
| | - Mallika Imwong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Ashenafi Assefa
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
- Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Awab Ghulam Rahim
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
- Afghan International Islamic University, Kabul, Afghanistan
| | - Hoang Chau Nguyen
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, 764 Vo Van Kiet, W.1, Dist.5, Ho Chi Minh City, Vietnam
| | - Tinh Hien Tran
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, 764 Vo Van Kiet, W.1, Dist.5, Ho Chi Minh City, Vietnam
| | | | - Gavin C K W Koh
- Department of Infectious Diseases, Northwick Park Hospital, Harrow, UK
| | - Nicholas J White
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7LJ, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Nicholas Day
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7LJ, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | | | - Julian C Rayner
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, CB2 0XY, UK
| | - Ric N Price
- Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, 0811, Australia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7LJ, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Sarah Auburn
- Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, 0811, Australia.
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7LJ, UK.
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Cabrera-Sosa L, Nolasco O, Kattenberg JH, Fernandez-Miñope C, Valdivia HO, Barazorda K, Arévalo de Los Rios S, Rodriguez-Ferrucci H, Vinetz JM, Rosanas-Urgell A, Van Geertruyden JP, Gamboa D, Delgado-Ratto C. Genomic surveillance of malaria parasites in an indigenous community in the Peruvian Amazon. Sci Rep 2024; 14:16291. [PMID: 39009685 PMCID: PMC11250820 DOI: 10.1038/s41598-024-66925-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 07/05/2024] [Indexed: 07/17/2024] Open
Abstract
Hard-to-reach communities represent Peru's main challenge for malaria elimination, but information about transmission in these areas is scarce. Here, we assessed Plasmodium vivax (Pv) and P. falciparum (Pf) transmission dynamics, resistance markers, and Pf hrp2/3 deletions in Nueva Jerusalén (NJ), a remote, indigenous community in the Peruvian Amazon with high population mobility. We collected samples from November 2019 to May 2020 by active (ACD) and passive case detection (PCD) in NJ. Parasites were identified with microscopy and PCR. Then, we analyzed a representative set of positive-PCR samples (Pv = 68, Pf = 58) using highly-multiplexed deep sequencing assays (AmpliSeq) and compared NJ parasites with ones from other remote Peruvian areas using population genetics indexes. The ACD intervention did not reduce malaria cases in the short term, and persistent malaria transmission was observed (at least one Pv infection was detected in 96% of the study days). In Nueva Jerusalen, the Pv population had modest genetic diversity (He = 0.27). Pf population had lower diversity (He = 0.08) and presented temporal clustering, one of these clusters linked to an outbreak in February 2020. Moreover, Pv and Pf parasites from NJ exhibited variable levels of differentiation (Pv Fst = 0.07-0.52 and Pf Fst = 0.11-0.58) with parasites from other remote areas. No artemisin resistance mutations but chloroquine (57%) and sulfadoxine-pyrimethamine (35-67%) were detected in NJ's Pf parasites. Moreover, pfhrp2/3 gene deletions were common (32-50% of parasites with one or both genes deleted). The persistent Pv transmission and the detection of a Pf outbreak with parasites genetically distinct from the local ones highlight the need for tailored interventions focusing on mobility patterns and imported infections in remote areas to eliminate malaria in the Peruvian Amazon.
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Affiliation(s)
- Luis Cabrera-Sosa
- Laboratorio de Malaria: Parásitos y Vectores, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru.
- Instituto de Medicina Tropical "Alexander Von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru.
| | - Oscar Nolasco
- Laboratorio de Malaria: Parásitos y Vectores, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Johanna H Kattenberg
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Carlos Fernandez-Miñope
- Instituto de Medicina Tropical "Alexander Von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru
- Malaria Research Group (MaRch), Global Health Institute (GHI), Family Medicine and Population Health Department (FAMPOP), Faculty of Medicine, University of Antwerp, Antwerp, Belgium
| | - Hugo O Valdivia
- Department of Parasitology, U.S. Naval Medical Research Unit SOUTH (NAMRU SOUTH), Lima, Peru
| | - Keare Barazorda
- Department of Parasitology, U.S. Naval Medical Research Unit SOUTH (NAMRU SOUTH), Lima, Peru
| | | | - Hugo Rodriguez-Ferrucci
- Facultad de Medicina Humana, Universidad Nacional de la Amazonía Peruana, Iquitos, Loreto, Peru
| | - Joseph M Vinetz
- Instituto de Medicina Tropical "Alexander Von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Anna Rosanas-Urgell
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Jean-Pierre Van Geertruyden
- Malaria Research Group (MaRch), Global Health Institute (GHI), Family Medicine and Population Health Department (FAMPOP), Faculty of Medicine, University of Antwerp, Antwerp, Belgium
| | - Dionicia Gamboa
- Laboratorio de Malaria: Parásitos y Vectores, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
- Instituto de Medicina Tropical "Alexander Von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Christopher Delgado-Ratto
- Instituto de Medicina Tropical "Alexander Von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru.
- Malaria Research Group (MaRch), Global Health Institute (GHI), Family Medicine and Population Health Department (FAMPOP), Faculty of Medicine, University of Antwerp, Antwerp, Belgium.
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Kattenberg JH, Cabrera-Sosa L, Figueroa-Ildefonso E, Mutsaers M, Monsieurs P, Guetens P, Infante B, Delgado-Ratto C, Gamboa D, Rosanas-Urgell A. Plasmodium vivax genomic surveillance in the Peruvian Amazon with Pv AmpliSeq assay. PLoS Negl Trop Dis 2024; 18:e0011879. [PMID: 38991038 PMCID: PMC11265702 DOI: 10.1371/journal.pntd.0011879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 07/23/2024] [Accepted: 06/12/2024] [Indexed: 07/13/2024] Open
Abstract
BACKGROUND Plasmodium vivax is the most predominant malaria species in Latin America, constituting 71.5% of malaria cases in 2021. With several countries aiming for malaria elimination, it is crucial to prioritize effectiveness of national control programs by optimizing the utilization of available resources and strategically implementing necessary changes. To support this, there is a need for innovative approaches such as genomic surveillance tools that can investigate changes in transmission intensity, imported cases and sources of reintroduction, and can detect molecular markers associated with drug resistance. METHODOLOGY/PRINCIPAL FINDINGS Here, we apply a modified highly-multiplexed deep sequencing assay: Pv AmpliSeq v2 Peru. The tool targets a newly developed 41-SNP Peru barcode for parasite population analysis within Peru, the 33-SNP vivaxGEN-geo panel for country-level classification, and 11 putative drug resistance genes. It was applied to 230 samples from the Peruvian Amazon (2007-2020), generating baseline surveillance data. We observed a heterogenous P. vivax population with high diversity and gene flow in peri-urban areas of Maynas province (Loreto region) with a temporal drift using all SNPs detected by the assay (nSNP = 2909). In comparison, in an indigenous isolated area, the parasite population was genetically differentiated (FST = 0.07-0.09) with moderate diversity and high relatedness between isolates in the community. In a remote border community, a clonal P. vivax cluster was identified, with distinct haplotypes in drug resistant genes and ama1, more similar to Brazilian isolates, likely representing an introduction of P. vivax from Brazil at that time. To test its applicability for Latin America, we evaluated the SNP Peru barcode in P. vivax genomes from the region and demonstrated the capacity to capture local population clustering at within-country level. CONCLUSIONS/SIGNIFICANCE Together this data shows that P. vivax transmission is heterogeneous in different settings within the Peruvian Amazon. Genetic analysis is a key component for regional malaria control, offering valuable insights that should be incorporated into routine surveillance.
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Affiliation(s)
| | - Luis Cabrera-Sosa
- Instituto de Medicina Tropical "Alexander von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru
- Laboratorio de Malaria: Parásitos y Vectores, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
- Malaria Research Group (MaRCH), Global Health Institute, Faculty of Medicine, University of Antwerp, Antwerp, Belgium
| | - Erick Figueroa-Ildefonso
- Instituto de Medicina Tropical "Alexander von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru
- Laboratorio de Malaria: Parásitos y Vectores, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mathijs Mutsaers
- Malariology Unit, Biomedical Sciences Department, Institute of Tropical Medicine, Antwerp, Belgium
| | - Pieter Monsieurs
- Malariology Unit, Biomedical Sciences Department, Institute of Tropical Medicine, Antwerp, Belgium
| | - Pieter Guetens
- Malariology Unit, Biomedical Sciences Department, Institute of Tropical Medicine, Antwerp, Belgium
| | - Berónica Infante
- Instituto de Medicina Tropical "Alexander von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru
- Laboratorio de Malaria: Parásitos y Vectores, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Christopher Delgado-Ratto
- Malaria Research Group (MaRCH), Global Health Institute, Faculty of Medicine, University of Antwerp, Antwerp, Belgium
| | - Dionicia Gamboa
- Instituto de Medicina Tropical "Alexander von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru
- Laboratorio de Malaria: Parásitos y Vectores, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
- Departamento de Ciencias Celulares y Moleculares, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Anna Rosanas-Urgell
- Malariology Unit, Biomedical Sciences Department, Institute of Tropical Medicine, Antwerp, Belgium
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Popkin-Hall ZR, Niaré K, Crudale R, Simkin A, Fola AA, Sanchez JF, Pannebaker DL, Giesbrecht DJ, Kim IE, Aydemir Ö, Bailey JA, Valdivia HO, Juliano JJ. High-Throughput Genotyping of Plasmodium vivax in the Peruvian Amazon via Molecular Inversion Probes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.27.24309599. [PMID: 38978652 PMCID: PMC11230302 DOI: 10.1101/2024.06.27.24309599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Plasmodium vivax transmission occurs throughout the tropics and is an emerging threat in areas of Plasmodium falciparum decline, causing relapse infections that complicate treatment and control. Targeted sequencing for P. falciparum has been widely deployed to detect population structure and the geographic spread of antimalarial and diagnostic resistance. However, there are fewer such tools for P. vivax . Leveraging global variation data, we designed four molecular inversion probe (MIP) genotyping panels targeting geographically differentiating SNPs, neutral SNPs, putative antimalarial resistance genes, and vaccine candidate genes. We deployed these MIP panels on 866 infections from the Peruvian Amazon and identified transmission networks with clonality (IBD>0.99), copy number variation in Pvdbp and multiple Pvrbps , fixation of putative antimalarial resistance, and balancing selection in 13 vaccine candidate genes. Our MIP panels are the broadest genotyping panel currently available and are poised for successful deployment in other regions of P. vivax transmission.
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Janko MM, Araujo AL, Ascencio EJ, Guedes GR, Vasco LE, Santos RO, Damasceno CP, Medrano PG, Chacón-Uscamaita PR, Gunderson AK, O'Malley S, Kansara PH, Narvaez MB, Coombes C, Pizzitutti F, Salmon-Mulanovich G, Zaitchik BF, Mena CF, Lescano AG, Barbieri AF, Pan WK. Study protocol: improving response to malaria in the Amazon through identification of inter-community networks and human mobility in border regions of Ecuador, Peru and Brazil. BMJ Open 2024; 14:e078911. [PMID: 38626977 PMCID: PMC11029361 DOI: 10.1136/bmjopen-2023-078911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 02/29/2024] [Indexed: 04/19/2024] Open
Abstract
INTRODUCTION Understanding human mobility's role in malaria transmission is critical to successful control and elimination. However, common approaches to measuring mobility are ill-equipped for remote regions such as the Amazon. This study develops a network survey to quantify the effect of community connectivity and mobility on malaria transmission. METHODS We measure community connectivity across the study area using a respondent driven sampling design among key informants who are at least 18 years of age. 45 initial communities will be selected: 10 in Brazil, 10 in Ecuador and 25 in Peru. Participants will be recruited in each initial node and administered a survey to obtain data on each community's mobility patterns. Survey responses will be ranked and the 2-3 most connected communities will then be selected and surveyed. This process will be repeated for a third round of data collection. Community network matrices will be linked with each country's malaria surveillance system to test the effects of mobility on disease risk. ETHICS AND DISSEMINATION This study protocol has been approved by the institutional review boards of Duke University (USA), Universidad San Francisco de Quito (Ecuador), Universidad Peruana Cayetano Heredia (Peru) and Universidade Federal Minas Gerais (Brazil). Results will be disseminated in communities by the end of the study.
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Affiliation(s)
- Mark M Janko
- Duke Global Health Institute, Durham, North Carolina, USA
| | - Andrea L Araujo
- Instituto de Geografia, Universidad San Francisco de Quito, Quito, Ecuador
| | - Edson J Ascencio
- Emerge, Emerging Diseases and Climate Change Research Unit, School of Public Health and Administration, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Gilvan R Guedes
- Center for Regional Development and Planning (Cedeplar), Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Luis E Vasco
- Instituto de Geografia, Universidad San Francisco de Quito, Quito, Ecuador
| | - Reinaldo O Santos
- Center for Regional Development and Planning (Cedeplar), Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Camila P Damasceno
- Center for Regional Development and Planning (Cedeplar), Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
| | | | - Pamela R Chacón-Uscamaita
- Emerge, Emerging Diseases and Climate Change Research Unit, School of Public Health and Administration, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Annika K Gunderson
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sara O'Malley
- Duke University Nicholas School of the Environment, Durham, North Carolina, USA
| | - Prakrut H Kansara
- Department of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, Maryland, USA
| | - Manuel B Narvaez
- Instituto de Geografia, Universidad San Francisco de Quito, Quito, Ecuador
| | - Carolina Coombes
- Emerge, Emerging Diseases and Climate Change Research Unit, School of Public Health and Administration, Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | | | - Benjamin F Zaitchik
- Department of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, Maryland, USA
| | - Carlos F Mena
- Instituto de Geografia, Universidad San Francisco de Quito, Quito, Ecuador
| | - Andres G Lescano
- Emerge, Emerging Diseases and Climate Change Research Unit, School of Public Health and Administration, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Alisson F Barbieri
- Center for Regional Development and Planning (Cedeplar), Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - William K Pan
- Duke Global Health Institute, Durham, North Carolina, USA
- Duke University Nicholas School of the Environment, Durham, North Carolina, USA
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Kattenberg JH, Monsieurs P, De Meyer J, De Meulenaere K, Sauve E, de Oliveira TC, Ferreira MU, Gamboa D, Rosanas‐Urgell A. Population genomic evidence of structured and connected Plasmodium vivax populations under host selection in Latin America. Ecol Evol 2024; 14:e11103. [PMID: 38529021 PMCID: PMC10961478 DOI: 10.1002/ece3.11103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/15/2024] [Accepted: 02/20/2024] [Indexed: 03/27/2024] Open
Abstract
Pathogen genomic epidemiology has the potential to provide a deep understanding of population dynamics, facilitating strategic planning of interventions, monitoring their impact, and enabling timely responses, and thereby supporting control and elimination efforts of parasitic tropical diseases. Plasmodium vivax, responsible for most malaria cases outside Africa, shows high genetic diversity at the population level, driven by factors like sub-patent infections, a hidden reservoir of hypnozoites, and early transmission to mosquitoes. While Latin America has made significant progress in controlling Plasmodium falciparum, it faces challenges with residual P. vivax. To characterize genetic diversity and population structure and dynamics, we have analyzed the largest collection of P. vivax genomes to date, including 1474 high-quality genomes from 31 countries across Asia, Africa, Oceania, and America. While P. vivax shows high genetic diversity globally, Latin American isolates form a distinctive population, which is further divided into sub-populations and occasional clonal pockets. Genetic diversity within the continent was associated with the intensity of transmission. Population differentiation exists between Central America and the North Coast of South America, vs. the Amazon Basin, with significant gene flow within the Amazon Basin, but limited connectivity between the Northwest Coast and the Amazon Basin. Shared genomic regions in these parasite populations indicate adaptive evolution, particularly in genes related to DNA replication, RNA processing, invasion, and motility - crucial for the parasite's survival in diverse environments. Understanding these population-level adaptations is crucial for effective control efforts, offering insights into potential mechanisms behind drug resistance, immune evasion, and transmission dynamics.
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Affiliation(s)
| | - Pieter Monsieurs
- Malariology UnitInstitute of Tropical Medicine AntwerpAntwerpBelgium
| | - Julie De Meyer
- Malariology UnitInstitute of Tropical Medicine AntwerpAntwerpBelgium
- Present address:
Integrated Molecular Plant physiology Research (IMPRES) and Plants and Ecosystems (PLECO), Department of BiologyUniversity of AntwerpAntwerpBelgium
| | | | - Erin Sauve
- Malariology UnitInstitute of Tropical Medicine AntwerpAntwerpBelgium
| | - Thaís C. de Oliveira
- Department of Parasitology, Institute of Biomedical SciencesUniversity of São PauloSão PauloBrazil
| | - Marcelo U. Ferreira
- Department of Parasitology, Institute of Biomedical SciencesUniversity of São PauloSão PauloBrazil
- Global Health and Tropical Medicine, Institute of Hygiene and Tropical MedicineNova University of LisbonLisbonPortugal
| | - Dionicia Gamboa
- Instituto de Medicina Tropical “Alexander von Humboldt”Universidad Peruana Cayetano HerediaLimaPeru
- Laboratorio de Malaria: Parásitos y Vectores, Laboratorios de Investigación y Desarrollo, Departamento de Ciencias Celulares y Moleculares, Facultad de Ciencias e IngenieríaUniversidad Peruana Cayetano HerediaLimaPeru
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Cabrera-Sosa L, Nolasco O, Kattenberg JH, Fernandez-Miñope C, Valdivia HO, Barazorda K, Rios SADL, Rodriguez-Ferrucci H, Vinetz JM, Rosanas-Urgell A, Geertruyden JPV, Gamboa D, Delgado-Ratto C. Genomic surveillance of malaria parasites in an indigenous community in the Peruvian Amazon. RESEARCH SQUARE 2024:rs.3.rs-3979991. [PMID: 38464169 PMCID: PMC10925399 DOI: 10.21203/rs.3.rs-3979991/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Hard-to-reach communities represent Peru's main challenge for malaria elimination, but information about transmission in these areas is scarce. Here, we assessed Plasmodium vivax (Pv) and P. falciparum (Pf) transmission dynamics, resistance markers, and Pf hrp2/3 deletions in Nueva Jerusalén (NJ), a remote, indigenous community in the Peruvian Amazon with high population mobility. We collected samples from November 2019 to May 2020 by active (ACD) and passive case detection (PCD) in NJ. Parasites were identified with microscopy and PCR. Then, we analyzed a representative set of positive-PCR samples (Pv = 68, Pf = 58) using highly-multiplexed deep sequencing assays (AmpliSeq) and compared NJ parasites with ones from other remote Peruvian areas using population genetics indexes. The ACD intervention did not reduce malaria cases in the short term, and persistent malaria transmission was observed (at least one Pv infection was detected in 96% of the study days). In Nueva Jerusalen, the Pv population had modest genetic diversity (He = 0.27). Pf population had lower diversity (He = 0.08) and presented temporal clustering, one of these clusters linked to an outbreak in February 2020. Moreover, Pv and Pf parasites from NJ exhibited variable levels of differentiation (Pv Fst = -0.52 & Pf Fst = 0.11-0.58) with parasites from other remote areas. No artemisin resistance mutations but chloroquine (57%) and sulfadoxine-pyrimethamine (35-67%) were detected in NJ's Pf parasites. Moreover, pfhrp2/3 gene deletions were common (32-50% of parasites with one or both genes deleted). The persistent Pv transmission and the detection of a Pf outbreak with parasites genetically distinct from the local ones highlight the need for tailored interventions focusing on mobility patterns and imported infections in remote areas to eliminate malaria in the Peruvian Amazon.
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Affiliation(s)
- Luis Cabrera-Sosa
- Laboratorio de Malaria: Parásitos y Vectores, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia
| | - Oscar Nolasco
- Laboratorio de Malaria: Parásitos y Vectores, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia
| | | | - Carlos Fernandez-Miñope
- Malaria Research group (MaRch), Global Health Institute, Family Medicine and Population Health department, Faculty of Medicine, University of Antwerp
| | - Hugo O Valdivia
- Department of Parasitology, U.S. Naval Medical Research Unit SOUTH (NAMRU SOUTH)
| | - Keare Barazorda
- Department of Parasitology, U.S. Naval Medical Research Unit SOUTH (NAMRU SOUTH)
| | | | | | - Joseph M Vinetz
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine
| | | | - Jean-Pierre Van Geertruyden
- Malaria Research group (MaRch), Global Health Institute, Family Medicine and Population Health department, Faculty of Medicine, University of Antwerp
| | - Dionicia Gamboa
- Laboratorio de Malaria: Parásitos y Vectores, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia
| | - Christopher Delgado-Ratto
- Malaria Research group (MaRch), Global Health Institute, Family Medicine and Population Health department, Faculty of Medicine, University of Antwerp
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9
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Janko MM, Araujo AL, Ascencio EJ, Guedes GR, Vasco LE, Santos RA, Damasceno CP, Medrano PG, Chacón-Uscamaita PR, Gunderson AK, O’Malley S, Kansara PH, Narvaez MB, Coombes CS, Pizzitutti F, Salmon-Mulanovich G, Zaitchik BF, Mena CF, Lescano AG, Barbieri AF, Pan WK. Network Profile: Improving Response to Malaria in the Amazon through Identification of Inter-Community Networks and Human Mobility in Border Regions of Ecuador, Peru, and Brazil. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.29.23299202. [PMID: 38076857 PMCID: PMC10705622 DOI: 10.1101/2023.11.29.23299202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Objectives Understanding human mobility's role on malaria transmission is critical to successful control and elimination. However, common approaches to measuring mobility are ill-equipped for remote regions such as the Amazon. This study develops a network survey to quantify the effect of community connectivity and mobility on malaria transmission. Design A community-level network survey. Setting We collect data on community connectivity along three river systems in the Amazon basin: the Pastaza river corridor spanning the Ecuador-Peru border; and the Amazon and Javari river corridors spanning the Brazil-Peru border. Participants We interviewed key informants in Brazil, Ecuador, and Peru, including from indigenous communities: Shuar, Achuar, Shiwiar, Kichwa, Ticuna, and Yagua. Key informants are at least 18 years of age and are considered community leaders. Primary outcome Weekly, community-level malaria incidence during the study period. Methods We measure community connectivity across the study area using a respondent driven sampling design. Forty-five communities were initially selected: 10 in Brazil, 10 in Ecuador, and 25 in Peru. Participants were recruited in each initial node and administered a survey to obtain data on each community's mobility patterns. Survey responses were ranked and the 2-3 most connected communities were then selected and surveyed. This process was repeated for a third round of data collection. Community network matrices will be linked with eadch country's malaria surveillance system to test the effects of mobility on disease risk. Findings To date, 586 key informants were surveyed from 126 communities along the Pastaza river corridor. Data collection along the Amazon and Javari river corridors is ongoing. Initial results indicate that network sampling is a superior method to delineate migration flows between communities. Conclusions Our study provides measures of mobility and connectivity in rural settings where traditional approaches are insufficient, and will allow us to understand mobility's effect on malaria transmission.
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Affiliation(s)
- Mark M. Janko
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA
| | - Andrea L. Araujo
- Instituto de Geografía, Universidad San Francisco de Quito, Quito, Ecuador
| | - Edson J. Ascencio
- Emerge, Emerging Diseases and Climate Change Research Unit, School of Public Health and Administration, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Gilvan R. Guedes
- Center for Regional Development and Planning (Cedeplar), Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Luis E. Vasco
- Instituto de Geografía, Universidad San Francisco de Quito, Quito, Ecuador
| | - Reinaldo A. Santos
- Center for Regional Development and Planning (Cedeplar), Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Camila P. Damasceno
- Center for Regional Development and Planning (Cedeplar), Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Perla G. Medrano
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA
| | - Pamela R. Chacón-Uscamaita
- Emerge, Emerging Diseases and Climate Change Research Unit, School of Public Health and Administration, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Annika K. Gunderson
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sara O’Malley
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA
| | - Prakrut H. Kansara
- Department of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, Maryland, USA
| | - Manuel B. Narvaez
- Instituto de Geografía, Universidad San Francisco de Quito, Quito, Ecuador
| | - Carolina S. Coombes
- Emerge, Emerging Diseases and Climate Change Research Unit, School of Public Health and Administration, Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | | | - Benjamin F. Zaitchik
- Department of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, Maryland, USA
| | - Carlos F. Mena
- Instituto de Geografía, Universidad San Francisco de Quito, Quito, Ecuador
| | - Andres G. Lescano
- Emerge, Emerging Diseases and Climate Change Research Unit, School of Public Health and Administration, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Alisson F. Barbieri
- Center for Regional Development and Planning (Cedeplar), Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - William K. Pan
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA
- Nicholas School of the Environment, Duke University, Durham, North Carolina, USA
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De Meulenaere K, Cuypers B, Gamboa D, Laukens K, Rosanas-Urgell A. A new Plasmodium vivax reference genome for South American isolates. BMC Genomics 2023; 24:606. [PMID: 37821878 PMCID: PMC10568799 DOI: 10.1186/s12864-023-09707-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 09/30/2023] [Indexed: 10/13/2023] Open
Abstract
BACKGROUND Plasmodium vivax is the second most important cause of human malaria worldwide, and accounts for the majority of malaria cases in South America. A high-quality reference genome exists for Papua Indonesia (PvP01) and Thailand (PvW1), but is lacking for South America. A reference genome specifically for South America would be beneficial though, as P. vivax is a genetically diverse parasite with geographical clustering. RESULTS This study presents a new high-quality assembly of a South American P. vivax isolate, referred to as PvPAM (P. vivax Peruvian AMazon). The genome was obtained from a low input patient sample from the Peruvian Amazon and sequenced using PacBio technology, resulting in a highly complete assembly with 6497 functional genes. Telomeric ends were present in 17 out of 28 chromosomal ends, and additional (sub)telomeric regions are present in 12 unassigned contigs. A comparison of multigene families between PvPAM and the PvP01 genome revealed remarkable variation in vir genes, and the presence of merozoite surface proteins (MSP) 3.6 and 3.7. Three dhfr and dhps drug resistance associated mutations are present in PvPAM, similar to those found in other Peruvian isolates. Mapping of publicly available South American whole genome sequencing (WGS) data to PvPAM resulted in significantly fewer variants and truncated reads compared to the use of PvP01 or PvW1 as reference genomes. To minimize the number of core genome variants in non-South American samples, PvW1 is most suited for Southeast Asian isolates, both PvPAM and PvW1 are suited for South Asian isolates, and PvPAM is recommended for African isolates. Interestingly, non-South American samples still contained the least subtelomeric variants when mapped to PvPAM, indicating high quality of the PvPAM subtelomeric regions. CONCLUSIONS Our findings show that the PvPAM reference genome more accurately represents South American P. vivax isolates in comparison to PvP01 and PvW1. In addition, PvPAM has a high level of completeness, and contains a similar number of annotated genes as PvP01 or PvW1. The PvPAM genome therefore will be a valuable resource to improve future genomic analyses on P. vivax isolates from the South American continent.
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Affiliation(s)
- Katlijn De Meulenaere
- Department of Biomedical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium.
- Department of Computer Science, University of Antwerp, Antwerp, Belgium.
| | - Bart Cuypers
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
| | - Dionicia Gamboa
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Departamento de Ciencias Celulares y Moleculares, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Kris Laukens
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
| | - Anna Rosanas-Urgell
- Department of Biomedical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium.
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11
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Janko MM, Recalde-Coronel GC, Damasceno CP, Salmón-Mulanovich G, Barbieri AF, Lescano AG, Zaitchik BF, Pan WK. The impact of sustained malaria control in the Loreto region of Peru: a retrospective, observational, spatially-varying interrupted time series analysis of the PAMAFRO program. LANCET REGIONAL HEALTH. AMERICAS 2023; 20:100477. [PMID: 36970494 PMCID: PMC10036736 DOI: 10.1016/j.lana.2023.100477] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 10/23/2022] [Accepted: 03/07/2023] [Indexed: 03/18/2023]
Abstract
Background Although malaria control investments worldwide have resulted in dramatic declines in transmission since 2000, progress has stalled. In the Amazon, malaria resurgence has followed withdrawal of Global Fund support of the Project for Malaria Control in Andean Border Areas (PAMAFRO). We estimate intervention-specific and spatially-explicit effects of the PAMAFRO program on malaria incidence across the Loreto region of Peru, and consider the influence of the environmental risk factors in the presence of interventions. Methods We conducted a retrospective, observational, spatial interrupted time series analysis of malaria incidence rates among people reporting to health posts across Loreto, Peru between the first epidemiological week of January 2001 and the last epidemiological week of December 2016. Model inference is at the smallest administrative unit (district), where the weekly number of diagnosed cases of Plasmodium vivax and Plasmodium falciparum were determined by microscopy. Census data provided population at risk. We include as covariates weekly estimates of minimum temperature and cumulative precipitation in each district, as well as spatially- and temporally-lagged malaria incidence rates. Environmental data were derived from a hydrometeorological model designed for the Amazon. We used Bayesian spatiotemporal modeling techniques to estimate the impact of the PAMAFRO program, variability in environmental effects, and the role of climate anomalies on transmission after PAMAFRO withdrawal. Findings During the PAMAFRO program, incidence of P. vivax declined from 42.8 to 10.1 cases/1000 people/year. Incidence for P. falciparum declined from 14.3 to 2.5 cases/1000 people/year over this same period. The effects of PAMAFRO-supported interventions varied both by geography and species of malaria. Interventions were only effective in districts where interventions were also deployed in surrounding districts. Further, interventions diminished the effects of other prevailing demographic and environmental risk factors. Withdrawal of the program led to a resurgence in transmission. Increasing minimum temperatures and variability and intensity of rainfall events from 2011 onward and accompanying population displacements contributed to this resurgence. Interpretation Malaria control programs must consider the climate and environmental scope of interventions to maximize effectiveness. They must also ensure financial sustainability to maintain local progress and commitment to malaria prevention and elimination efforts, as well as to offset the effects of environmental change that increase transmission risk. Funding National Aeronautics and Space Administration, National Institutes of Health, Bill and Melinda Gates Foundation.
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Affiliation(s)
- Mark M. Janko
- Duke Global Health Institute, Duke University, Durham, NC, USA
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, USA
| | - G. Cristina Recalde-Coronel
- Department of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, MD, USA
- Facultad de Ingeniería Marítima y Ciencias del Mar, Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador
| | | | | | | | - Andrés G. Lescano
- Clima, Latin American Center of Excellence for Climate Change and Health, and Emerge, Emerging Diseases and Climate Change Research Unit, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Benjamin F. Zaitchik
- Department of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, MD, USA
| | - William K. Pan
- Duke Global Health Institute, Duke University, Durham, NC, USA
- Nicholas School of the Environment, Duke University, Durham, NC, USA
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12
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Dombrowski JG, Acford-Palmer H, Campos M, Separovic EPM, Epiphanio S, Clark TG, Campino S, Marinho CRF. Genetic diversity of Plasmodium vivax isolates from pregnant women in the Western Brazilian Amazon: a prospective cohort study. LANCET REGIONAL HEALTH. AMERICAS 2023; 18:100407. [PMID: 36844021 PMCID: PMC9950542 DOI: 10.1016/j.lana.2022.100407] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/16/2022] [Accepted: 11/11/2022] [Indexed: 12/03/2022]
Abstract
Background Each year, 92 million pregnant women are at risk of contracting malaria during pregnancy, with the underestimation of the mortality and morbidity burden associated with Plasmodium vivax. During pregnancy, P. vivax infection is associated with low birth weight, maternal anaemia, premature delivery, and stillbirth. In the State of Acre (Brazil), high transmission leaves pregnant women at greater risk of contracting malaria and having a greater number of recurrences. The study of genetic diversity and the association of haplotypes with adverse pregnancy effects is of great importance for the control of the disease. Here we investigate the genetic diversity of P. vivax parasites infecting pregnant women across their pregnancies. Methods P. vivax DNA was extracted from 330 samples from 177 women followed during pregnancy, collected in the State of Acre, Brazil. All samples were negative for Plasmodium falciparum DNA. Sequence data for the Pvmsp1 gene was analysed alongside data from six microsatellite (MS) markers. Allelic frequencies, haplotype frequencies, expected heterozygosity (HE) were calculated. Whole genome sequencing (WGS) was conducted on four samples from pregnant women and phylogenetic analysis performed with other samples from South American regions. Findings Initially, the pregnant women were stratified into two groups-1 recurrence and 2 or more recurrences-in which no differences were observed in clinical gestational outcomes or in placental histological changes between the two groups. Then we evaluated the parasites genetically. An average of 18.5 distinct alleles were found at each of the MS loci, and the HE calculated for each marker indicates a high genetic diversity occurring within the population. There was a high percentage of polyclonal infections (61.7%, 108/175), and one haplotype (H1) occurred frequently (20%), with only 9 of the haplotypes appearing in more than one patient. Interpretation Most pregnant women had polyclonal infections that could be the result of relapses and/or re-infections. The high percentage of H1 parasites, along with the low frequency of many other haplotypes are suggestive of a clonal expansion. Phylogenetic analysis shows that P. vivax population within pregnant women clustered with other Brazilian samples in the region. Funding FAPESP and CNPq - Brazil.
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Affiliation(s)
| | - Holly Acford-Palmer
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Monica Campos
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | | | - Sabrina Epiphanio
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Taane Gregory Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
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13
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Carrasco-Escobar G, Rosado J, Nolasco O, White MT, Mueller I, Castro MC, Rodriguez-Ferruci H, Gamboa D, Llanos-Cuentas A, Vinetz JM, Benmarhnia T. Effect of out-of-village working activities on recent malaria exposure in the Peruvian Amazon using parametric g-formula. Sci Rep 2022; 12:19144. [PMID: 36351988 PMCID: PMC9645738 DOI: 10.1038/s41598-022-23528-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 11/01/2022] [Indexed: 11/11/2022] Open
Abstract
In the Amazon Region of Peru, occupational activities are important drivers of human mobility and may increase the individual risk of being infected while contributing to increasing malaria community-level transmission. Even though out-of-village working activities and other mobility patterns have been identified as determinants of malaria transmission, no studies have quantified the effect of out-of-village working activities on recent malaria exposure and proposed plausible intervention scenarios. Using two population-based cross-sectional studies in the Loreto Department in Peru, and the parametric g-formula method, we simulated various hypothetical scenarios intervening in out-of-village working activities to reflect their potential health benefits. This study estimated that the standardized mean outcome (malaria seroprevalence) in the unexposed population (no out-of-village workers) was 44.6% (95% CI: 41.7%-47.5%) and 66.7% (95% CI: 61.6%-71.8%) in the exposed population resulting in a risk difference of 22.1% (95% CI: 16.3%-27.9%). However, heterogeneous patterns in the effects of interest were observed between peri-urban and rural areas (Cochran's Q test = 15.5, p < 0.001). Heterogeneous patterns were also observed in scenarios of increased prevalence of out-of-village working activities and restriction scenarios by gender (male vs. female) and age (18 and under vs. 19 and older) that inform possible occupational interventions targetting population subgroups. The findings of this study support the hypothesis that targeting out-of-village workers will considerably benefit current malaria elimination strategies in the Amazon Region. Particularly, males and adult populations that carried out out-of-village working activities in rural areas contribute the most to the malaria seropositivity (recent exposure to the parasite) in the Peruvian Amazon.
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Affiliation(s)
- Gabriel Carrasco-Escobar
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA.
- Health Innovation Lab, Institute of Tropical Medicine "Alexander Von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru.
| | - Jason Rosado
- G5 Épidémiologie Et Analyse Des Maladies Infectieuses, Département de Santé Globale, Institut Pasteur, 75015, Paris, France
| | - Oscar Nolasco
- Instituto de Medicina Tropical Alexander Von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigación Y Desarrollo, Facultad de Ciencias Y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Michael T White
- G5 Épidémiologie Et Analyse Des Maladies Infectieuses, Département de Santé Globale, Institut Pasteur, 75015, Paris, France
| | - Ivo Mueller
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Marcia C Castro
- Department of Global Health and Population, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | - Dionicia Gamboa
- Instituto de Medicina Tropical Alexander Von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigación Y Desarrollo, Facultad de Ciencias Y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
- Departamento de Ciencias Celulares Y Moleculares, Facultad de Ciencias Y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Alejandro Llanos-Cuentas
- Instituto de Medicina Tropical Alexander Von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Joseph M Vinetz
- Instituto de Medicina Tropical Alexander Von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigación Y Desarrollo, Facultad de Ciencias Y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Tarik Benmarhnia
- Scripps Institution of Oceanography, University of California, San Diego, CA, 92037, USA
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14
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Villena FE, Sanchez JF, Nolasco O, Braga G, Ricopa L, Barazorda K, Salas CJ, Lucas C, Lizewski SE, Joya CA, Gamboa D, Delgado-Ratto C, Valdivia HO. Drug resistance and population structure of Plasmodium falciparum and Plasmodium vivax in the Peruvian Amazon. Sci Rep 2022; 12:16474. [PMID: 36182962 PMCID: PMC9526214 DOI: 10.1038/s41598-022-21028-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 09/21/2022] [Indexed: 11/22/2022] Open
Abstract
Malaria is a major health problem in Peru despite substantial progress achieved by the ongoing malaria elimination program. This study explored the population genetics of 63 Plasmodium falciparum and 170 P. vivax cases collected in the Peruvian Amazon Basin between 2015 and 2019. Microscopy and PCR were used for malaria detection and positive samples were genotyped at neutral and drug resistance-associated regions. The P. falciparum population exhibited a low nucleotide diversity (π = 0.02) whereas the P. vivax population presented a higher genetic diversity (π = 0.34). All P. falciparum samples (n = 63) carried chloroquine (CQ) resistant mutations on Pfcrt. Most P. falciparum samples (53 out of 54) carried sulfadoxine (SD) resistant mutations on Pfdhfr and Pfdhps. No evidence was found of artemisinin resistance mutations on kelch13. Population structure showed that a single cluster accounted for 93.4% of the P. falciparum samples whereas three clusters were found for P. vivax. Our study shows a low genetic diversity for both species with significant differences in genetic sub-structuring. The high prevalence of CQ-resistance mutations could be a result of indirect selection pressures driven by the P. vivax treatment scheme. These results could be useful for public health authorities to safeguard the progress that Peru has achieved towards malaria elimination.
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Affiliation(s)
| | - Juan F Sanchez
- Department of Parasitology, U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Lima, Peru
| | - Oscar Nolasco
- Instituto de Medicina Tropical Alexander Von Humboldt, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Greys Braga
- Department of Parasitology, U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Lima, Peru
| | | | | | - Carola J Salas
- Department of Parasitology, U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Lima, Peru
| | - Carmen Lucas
- Department of Parasitology, U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Lima, Peru
| | - Stephen E Lizewski
- Department of Parasitology, U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Lima, Peru
| | - Christie A Joya
- Department of Parasitology, U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Lima, Peru
| | - Dionicia Gamboa
- Instituto de Medicina Tropical Alexander Von Humboldt, Universidad Peruana Cayetano Heredia, Lima, 31, Peru.,Departamento de Ciencias Celulares y Moleculares, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Christopher Delgado-Ratto
- Instituto de Medicina Tropical Alexander Von Humboldt, Universidad Peruana Cayetano Heredia, Lima, 31, Peru.,Malaria Research Group (MaRCH), Global Health Institute, University of Antwerp, 2610, Antwerp, Belgium
| | - Hugo O Valdivia
- Department of Parasitology, U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Lima, Peru.
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15
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Brashear AM, Cui L. Population genomics in neglected malaria parasites. Front Microbiol 2022; 13:984394. [PMID: 36160257 PMCID: PMC9493318 DOI: 10.3389/fmicb.2022.984394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Malaria elimination includes neglected human malaria parasites Plasmodium vivax, Plasmodium ovale spp., and Plasmodium malariae. Biological features such as association with low-density infection and the formation of hypnozoites responsible for relapse make their elimination challenging. Studies on these parasites rely primarily on clinical samples due to the lack of long-term culture techniques. With improved methods to enrich parasite DNA from clinical samples, whole-genome sequencing of the neglected malaria parasites has gained increasing popularity. Population genomics of more than 2200 P. vivax global isolates has improved our knowledge of parasite biology and host-parasite interactions, identified vaccine targets and potential drug resistance markers, and provided a new way to track parasite migration and introduction and monitor the evolutionary response of local populations to elimination efforts. Here, we review advances in population genomics for neglected malaria parasites, discuss how the rich genomic information is being used to understand parasite biology and epidemiology, and explore opportunities for the applications of malaria genomic data in malaria elimination practice.
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Nourani L, Abouie Mehrizi A, Zakeri S, Djadid ND. Untangling population structure and genetic diversity of reticulocyte binding protein 2b (PvRBP2b) erythrocytic stage vaccine candidate in worldwide Plasmodium vivax isolates. PLoS One 2022; 17:e0266067. [PMID: 35349608 PMCID: PMC8963568 DOI: 10.1371/journal.pone.0266067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 03/11/2022] [Indexed: 11/18/2022] Open
Abstract
BACKGROUNDS Plasmodium vivax is the predominant Plasmodium species distributed extensively in the Americas and Asia-Pacific areas. Encoded protein by Plasmodium vivax Reticulocyte Binding Proteins (PvRBPs) family member are of critical prominence to parasite invasion and have been considered the significant targets in development of malaria vaccine for the blood stage. As high genetic polymorphism of parasites may impede the effectiveness of vaccine development, more research to unraveling genetic polymorphism of pvrbp2b from various geographical regions seems indispensable to map the exact pattern of field isolates. METHODOLOGY/PRINCIPAL FINDINGS The aim of this study was to determine the sequences of Iranian pvrbp2b (nt: 502-1896) gene and then, to ascertain polymorphism of pvrbp2b gene, recombination, the level of genetic distances, evaluation of natural selection, and the prediction of B-cell epitopes of Iranian and global P. vivax isolates. Pvrbp2b partial gene was amplified and sequenced from 60 Iranian P. vivax isolates. Iranian pvrbp2b sequences as well as 95 published sequences from five countries were used to evaluate the genetic diversity and neutral evolution signature in worldwide scale. A total of 38 SNPs were identified among 60 Iranian pvrbp2b sequences (32 non-synonymous and 6 synonymous mutations), and 32 amino acid substitutions were observed in 29 positions as compared to Sal-1 sequence. Worldwide sequence analysis showed that 44 amino acid changes had occurred in 37 positions of which seven polymorphic sites had trimorphic mutations while the rest was dimorphic. The overall nucleotide diversity for Iranian isolates was 0.00431 ± 0.00091 while the level of nucleotide diversity was ranged from 0.00337 ± 0.00076 (Peru) to 0.00452 ± 0.00092 (Thailand) in global scale. CONCLUSIONS/SIGNIFICANCE Of amino acid substitutions, 12 replacements were located in the B-cell epitopes in which nine polymorphic sites were positioned in N-terminal and three polymorphic sites in predicted B-cell epitopes of C-terminal, signifying both variable and conserved epitopes for vaccine designing. Using the achieved outcome of the current investigation interrogate questions to the selection of conserved regions of pvrbp2b and understanding polymorphism and immune system pressure to pave a way for developing a vaccine based on PvRBP2b candidate antigen.
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Affiliation(s)
- Leila Nourani
- Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Pasteur Institute of Iran, Tehran, Iran
| | - Akram Abouie Mehrizi
- Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Pasteur Institute of Iran, Tehran, Iran
| | - Sedigheh Zakeri
- Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Pasteur Institute of Iran, Tehran, Iran
| | - Navid Dinparast Djadid
- Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Pasteur Institute of Iran, Tehran, Iran
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17
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Daron J, Boissière A, Boundenga L, Ngoubangoye B, Houze S, Arnathau C, Sidobre C, Trape JF, Durand P, Renaud F, Fontaine MC, Prugnolle F, Rougeron V. Population genomic evidence of Plasmodium vivax Southeast Asian origin. SCIENCE ADVANCES 2021; 7:7/18/eabc3713. [PMID: 33910900 PMCID: PMC8081369 DOI: 10.1126/sciadv.abc3713] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 03/10/2021] [Indexed: 05/15/2023]
Abstract
Plasmodium vivax is the most common and widespread human malaria parasite. It was recently proposed that P. vivax originates from sub-Saharan Africa based on the circulation of its closest genetic relatives (P. vivax-like) among African great apes. However, the limited number of genetic markers and samples investigated questions the robustness of this hypothesis. Here, we extensively characterized the genomic variations of 447 human P. vivax strains and 19 ape P. vivax-like strains collected worldwide. Phylogenetic relationships between human and ape Plasmodium strains revealed that P. vivax is a sister clade of P. vivax-like, not included within the radiation of P. vivax-like By investigating various aspects of P. vivax genetic variation, we identified several notable geographical patterns in summary statistics in function of the increasing geographic distance from Southeast Asia, suggesting that P. vivax may have derived from a single area in Asia through serial founder effects.
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Affiliation(s)
- Josquin Daron
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France.
| | - Anne Boissière
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France
| | - Larson Boundenga
- Centre Interdisciplinaire de Recherches Médicales de Franceville, Franceville, Gabon
| | | | - Sandrine Houze
- Service de Parasitologie-mycologie CNR du Paludisme, AP-HP Hôpital Bichat, 46 rue H. Huchard, 75877 Paris Cedex 18, France
| | - Celine Arnathau
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France
| | - Christine Sidobre
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
| | - Jean-François Trape
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
| | - Patrick Durand
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France
| | - François Renaud
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France
| | - Michael C Fontaine
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, Netherlands
| | - Franck Prugnolle
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France
| | - Virginie Rougeron
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France.
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France
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18
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Fernandez-Miñope C, Delgado-Ratto C, Contreras-Mancilla J, Ferrucci HR, Llanos-Cuentas A, Gamboa D, Van Geertruyden JP. Towards one standard treatment for uncomplicated Plasmodium falciparum and Plasmodium vivax malaria: Perspectives from and for the Peruvian Amazon. Int J Infect Dis 2021; 105:293-297. [PMID: 33596478 DOI: 10.1016/j.ijid.2021.02.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 11/29/2022] Open
Abstract
Malaria continues to wreak havoc in the Peruvian Amazon. Lengthy research efforts have brought important lessons on its particular epidemiology: the heterogeneous levels of transmission, the large reservoir of both asymptomatic and submicroscopic infections, the co-transmission of Plasmodium vivax and Plasmodium falciparum in the same areas, and the limitations of current diagnostics. Based on these features, the national elimination program could greatly benefit from simplified standard treatment, with the use of artemisinin-based combination therapy and even shorter schemes of primaquine maintaing the total dosing. It is acknowledged that there is some uncertainty regarding the true prevalence of glucose-6-phosphate dehydrogenase deficiency (G6PD) and genetic polymorphisms related to cytochrome P-450 isozyme 2D6 functioning. Once we have a better understanding, tafenoquine, whether or not in combination with a rapid G6PD enzyme test, may become a future pathway to eliminate the otherwise hidden reservoir of the P. vivax hypnozoite through one standard Plasmodium treatment.
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Affiliation(s)
- Carlos Fernandez-Miñope
- Global Health Institute, University of Antwerp, Antwerp, Belgium; Instituto de Medicina Tropical "Alexander von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru.
| | - Christopher Delgado-Ratto
- Global Health Institute, University of Antwerp, Antwerp, Belgium; Instituto de Medicina Tropical "Alexander von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru.
| | - Juan Contreras-Mancilla
- Instituto de Medicina Tropical "Alexander von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru.
| | | | - Alejandro Llanos-Cuentas
- Instituto de Medicina Tropical "Alexander von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru.
| | - Dionicia Gamboa
- Instituto de Medicina Tropical "Alexander von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru; Departamento de Ciencias Celulares y Moleculares, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru.
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19
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Kattenberg JH, Razook Z, Keo R, Koepfli C, Jennison C, Lautu-Gumal D, Fola AA, Ome-Kaius M, Barnadas C, Siba P, Felger I, Kazura J, Mueller I, Robinson LJ, Barry AE. Monitoring Plasmodium falciparum and Plasmodium vivax using microsatellite markers indicates limited changes in population structure after substantial transmission decline in Papua New Guinea. Mol Ecol 2020; 29:4525-4541. [PMID: 32985031 PMCID: PMC10008436 DOI: 10.1111/mec.15654] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 07/27/2020] [Indexed: 02/01/2023]
Abstract
Monitoring the genetic structure of pathogen populations may be an economical and sensitive approach to quantify the impact of control on transmission dynamics, highlighting the need for a better understanding of changes in population genetic parameters as transmission declines. Here we describe the first population genetic analysis of two major human malaria parasites, Plasmodium falciparum (Pf) and Plasmodium vivax (Pv), following nationwide distribution of long-lasting insecticide-treated nets (LLINs) in Papua New Guinea (PNG). Parasite isolates from pre- (2005-2006) and post-LLIN (2010-2014) were genotyped using microsatellite markers. Despite parasite prevalence declining substantially (East Sepik Province: Pf = 54.9%-8.5%, Pv = 35.7%-5.6%, Madang Province: Pf = 38.0%-9.0%, Pv: 31.8%-19.7%), genetically diverse and intermixing parasite populations remained. Pf diversity declined modestly post-LLIN relative to pre-LLIN (East Sepik: Rs = 7.1-6.4, HE = 0.77-0.71; Madang: Rs = 8.2-6.1, HE = 0.79-0.71). Unexpectedly, population structure present in pre-LLIN populations was lost post-LLIN, suggesting that more frequent human movement between provinces may have contributed to higher gene flow. Pv prevalence initially declined but increased again in one province, yet diversity remained high throughout the study period (East Sepik: Rs = 11.4-9.3, HE = 0.83-0.80; Madang: Rs = 12.2-14.5, HE = 0.85-0.88). Although genetic differentiation values increased between provinces over time, no significant population structure was observed at any time point. For both species, a decline in multiple infections and increasing clonal transmission and significant multilocus linkage disequilibrium post-LLIN were positive indicators of impact on the parasite population using microsatellite markers. These parameters may be useful adjuncts to traditional epidemiological tools in the early stages of transmission reduction.
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Affiliation(s)
- Johanna Helena Kattenberg
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Yagaum, Papua New Guinea
| | - Zahra Razook
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Raksmei Keo
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Cristian Koepfli
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Charlie Jennison
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Dulcie Lautu-Gumal
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Yagaum, Papua New Guinea.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Abebe A Fola
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Maria Ome-Kaius
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Yagaum, Papua New Guinea.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Céline Barnadas
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Yagaum, Papua New Guinea.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Peter Siba
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Ingrid Felger
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - James Kazura
- Centre for Global Health and Diseases, Case Western Reserve University, Cleveland, OH, USA
| | - Ivo Mueller
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia.,Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
| | - Leanne J Robinson
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Yagaum, Papua New Guinea.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia.,Disease Elimination, Burnet Institute, Melbourne, VIC, Australia
| | - Alyssa E Barry
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
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20
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Fola AA, Kattenberg E, Razook Z, Lautu-Gumal D, Lee S, Mehra S, Bahlo M, Kazura J, Robinson LJ, Laman M, Mueller I, Barry AE. SNP barcodes provide higher resolution than microsatellite markers to measure Plasmodium vivax population genetics. Malar J 2020; 19:375. [PMID: 33081815 PMCID: PMC7576724 DOI: 10.1186/s12936-020-03440-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 10/03/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Genomic surveillance of malaria parasite populations has the potential to inform control strategies and to monitor the impact of interventions. Barcodes comprising large numbers of single nucleotide polymorphism (SNP) markers are accurate and efficient genotyping tools, however may need to be tailored to specific malaria transmission settings, since 'universal' barcodes can lack resolution at the local scale. A SNP barcode was developed that captures the diversity and structure of Plasmodium vivax populations of Papua New Guinea (PNG) for research and surveillance. METHODS Using 20 high-quality P. vivax genome sequences from PNG, a total of 178 evenly spaced neutral SNPs were selected for development of an amplicon sequencing assay combining a series of multiplex PCRs and sequencing on the Illumina MiSeq platform. For initial testing, 20 SNPs were amplified in a small number of mono- and polyclonal P. vivax infections. The full barcode was then validated by genotyping and population genetic analyses of 94 P. vivax isolates collected between 2012 and 2014 from four distinct catchment areas on the highly endemic north coast of PNG. Diversity and population structure determined from the SNP barcode data was then benchmarked against that of ten microsatellite markers used in previous population genetics studies. RESULTS From a total of 28,934,460 reads generated from the MiSeq Illumina run, 87% mapped to the PvSalI reference genome with deep coverage (median = 563, range 56-7586) per locus across genotyped samples. Of 178 SNPs assayed, 146 produced high-quality genotypes (minimum coverage = 56X) in more than 85% of P. vivax isolates. No amplification bias was introduced due to either polyclonal infection or whole genome amplification (WGA) of samples before genotyping. Compared to the microsatellite panels, the SNP barcode revealed greater variability in genetic diversity between populations and geographical population structure. The SNP barcode also enabled assignment of genotypes according to their geographic origins with a significant association between genetic distance and geographic distance at the sub-provincial level. CONCLUSIONS High-throughput SNP barcoding can be used to map variation of malaria transmission dynamics at sub-national resolution. The low cost per sample and genotyping strategy makes the transfer of this technology to field settings highly feasible.
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Affiliation(s)
- Abebe A Fola
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Eline Kattenberg
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
- Malariology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Zahra Razook
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- IMPACT Institute for Innovation in Mental and Physical Health and Clinical Translation, Deakin University, 75 Pigdons Road, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Dulcie Lautu-Gumal
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
- Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
- Disease Elimination Program, Burnet Institute, Melbourne, VIC, Australia
- IMPACT Institute for Innovation in Mental and Physical Health and Clinical Translation, Deakin University, 75 Pigdons Road, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Stuart Lee
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Somya Mehra
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Disease Elimination Program, Burnet Institute, Melbourne, VIC, Australia
- IMPACT Institute for Innovation in Mental and Physical Health and Clinical Translation, Deakin University, 75 Pigdons Road, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - James Kazura
- Disease Elimination Program, Burnet Institute, Melbourne, VIC, Australia
- Centre for Global Health and Diseases, Case Western Reserve University, Cleveland, Ohio, USA
| | - Leanne J Robinson
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
- Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
- Disease Elimination Program, Burnet Institute, Melbourne, VIC, Australia
| | - Moses Laman
- Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - Ivo Mueller
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
- Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
| | - Alyssa E Barry
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia.
- Disease Elimination Program, Burnet Institute, Melbourne, VIC, Australia.
- IMPACT Institute for Innovation in Mental and Physical Health and Clinical Translation, Deakin University, 75 Pigdons Road, Waurn Ponds, Geelong, VIC, 3216, Australia.
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21
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Carrasco-Escobar G, Fornace K, Wong D, Padilla-Huamantinco PG, Saldaña-Lopez JA, Castillo-Meza OE, Caballero-Andrade AE, Manrique E, Ruiz-Cabrejos J, Barboza JL, Rodriguez H, Henostroza G, Gamboa D, Castro MC, Vinetz JM, Llanos-Cuentas A. Open-Source 3D Printable GPS Tracker to Characterize the Role of Human Population Movement on Malaria Epidemiology in River Networks: A Proof-of-Concept Study in the Peruvian Amazon. Front Public Health 2020; 8:526468. [PMID: 33072692 PMCID: PMC7542225 DOI: 10.3389/fpubh.2020.526468] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 08/21/2020] [Indexed: 11/13/2022] Open
Abstract
Human movement affects malaria epidemiology at multiple geographical levels; however, few studies measure the role of human movement in the Amazon Region due to the challenging conditions and cost of movement tracking technologies. We developed an open-source low-cost 3D printable GPS-tracker and used this technology in a cohort study to characterize the role of human population movement in malaria epidemiology in a rural riverine village in the Peruvian Amazon. In this pilot study of 20 participants (mean age = 40 years old), 45,980 GPS coordinates were recorded over 1 month. Characteristic movement patterns were observed relative to the infection status and occupation of the participants. Applying two analytical animal movement ecology methods, utilization distributions (UDs) and integrated step selection functions (iSSF), we showed contrasting environmental selection and space use patterns according to infection status. These data suggested an important role of human movement in the epidemiology of malaria in the Peruvian Amazon due to high connectivity between villages of the same riverine network, suggesting limitations of current community-based control strategies. We additionally demonstrate the utility of this low-cost technology with movement ecology analysis to characterize human movement in resource-poor environments.
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Affiliation(s)
- Gabriel Carrasco-Escobar
- Health Innovation Laboratory, Institute of Tropical Medicine "Alexander von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru.,Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA, United States.,Laboratorio ICEMR-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Kimberly Fornace
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Daniel Wong
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Pierre G Padilla-Huamantinco
- Health Innovation Laboratory, Institute of Tropical Medicine "Alexander von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru.,Departamento de Ingenieria, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Jose A Saldaña-Lopez
- Departamento de Ingenieria, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Ober E Castillo-Meza
- Departamento de Ingenieria, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Armando E Caballero-Andrade
- Departamento de Ingenieria, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Edgar Manrique
- Health Innovation Laboratory, Institute of Tropical Medicine "Alexander von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru.,Laboratorio ICEMR-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Jorge Ruiz-Cabrejos
- Health Innovation Laboratory, Institute of Tropical Medicine "Alexander von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru.,Laboratorio ICEMR-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Jose Luis Barboza
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | - German Henostroza
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Dionicia Gamboa
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru.,Departamento de Ciencias Celulares y Moleculares, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru.,Instituto de Medicinal Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Marcia C Castro
- Department of Global Health and Population, Harvard T. H. Chan School of Public Health, Boston, MA, United States
| | - Joseph M Vinetz
- Instituto de Medicinal Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru.,Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, United States
| | - Alejandro Llanos-Cuentas
- Instituto de Medicinal Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru.,Facultad de Salud Pública y Administración, Universidad Peruana Cayetano Heredia, Lima, Peru
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22
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Dewasurendra RL, Baniecki ML, Schaffner S, Siriwardena Y, Moon J, Doshi R, Gunawardena S, Daniels RF, Neafsey D, Volkman S, Chandrasekharan NV, Wirth DF, Karunaweera ND. Use of a Plasmodium vivax genetic barcode for genomic surveillance and parasite tracking in Sri Lanka. Malar J 2020; 19:342. [PMID: 32958025 PMCID: PMC7504840 DOI: 10.1186/s12936-020-03386-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 08/25/2020] [Indexed: 11/18/2022] Open
Abstract
Background Sri Lanka was certified as a malaria-free nation in 2016; however, imported malaria cases continue to be reported. Evidence-based information on the genetic structure/diversity of the parasite populations is useful to understand the population history, assess the trends in transmission patterns, as well as to predict threatening phenotypes that may be introduced and spread in parasite populations disrupting elimination programmes. This study used a previously developed Plasmodium vivax single nucleotide polymorphism (SNP) barcode to evaluate the population dynamics of P. vivax parasite isolates from Sri Lanka and to assess the ability of the SNP barcode for tracking the parasites to its origin. Methods A total of 51 P. vivax samples collected during 2005–2011, mainly from three provinces of the country, were genotyped for 40 previously identified P. vivax SNPs using a high-resolution melting (HRM), single-nucleotide barcode method. Minor allele frequencies, linkage disequilibrium, pair-wise FST values, and complexity of infection (COI) were evaluated to determine the genetic diversity. Structure analysis was carried out using STRUCTURE software (Version 2.3.4) and SNP barcode was used to identify the genetic diversity of the local parasite populations collected from different years. Principal component analysis (PCA) was used to determine the clustering according to global geographic regions. Results The proportion of multi-clone infections was significantly higher in isolates collected during an infection outbreak in year 2007. The minor allele frequencies of the SNPs changed dramatically from year to year. Significant linkage was observed in sample sub-sets from years 2005 and 2007. The majority of the isolates from 2007 consisted of at least two genetically distinct parasite strains. The overall percentage of multi-clone infections for the entire parasite sample was 39.21%. Analysis using STRUCTURE software (Version 2.3.4) revealed the high genetic diversity of the sample sub-set from year 2007. In-silico analysis of these data with those available from other global geographical regions using PCA showed distinct clustering of parasite isolates according to geography, demonstrating the usefulness of the barcode in determining an isolate to be indigenous. Conclusions Plasmodium vivax parasite isolates collected during a disease outbreak in year 2007 were more genetically diverse compared to those collected from other years. In-silico analysis using the 40 SNP barcode is a useful tool to track the origin of an isolate of uncertain origin, especially to differentiate indigenous from imported cases. However, an extended barcode with more SNPs may be needed to distinguish highly clonal populations within the country.
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Affiliation(s)
- Rajika L Dewasurendra
- Department of Parasitology, Faculty of Medicine, University of Colombo, 25, Kynsey Road, Colombo 8, Sri Lanka
| | - Mary Lynn Baniecki
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Stephen Schaffner
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Yamuna Siriwardena
- Department of Parasitology, Faculty of Medicine, University of Colombo, 25, Kynsey Road, Colombo 8, Sri Lanka
| | - Jade Moon
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Boston, MA, 02138, USA
| | - R Doshi
- Department of Public Health, John Hopkins University, Baltimore, MD, 21218, USA
| | - Sharmini Gunawardena
- Department of Parasitology, Faculty of Medicine, University of Colombo, 25, Kynsey Road, Colombo 8, Sri Lanka
| | - Rachel F Daniels
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Daniel Neafsey
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Sarah Volkman
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | | | - Dyann F Wirth
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Nadira D Karunaweera
- Department of Parasitology, Faculty of Medicine, University of Colombo, 25, Kynsey Road, Colombo 8, Sri Lanka.
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23
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Rosas-Aguirre A, Guzman-Guzman M, Chuquiyauri R, Moreno M, Manrique P, Ramirez R, Carrasco-Escobar G, Rodriguez H, Speybroeck N, Conn JE, Gamboa D, Vinetz JM, Llanos-Cuentas A. Temporal and Microspatial Heterogeneity in Transmission Dynamics of Coendemic Plasmodium vivax and Plasmodium falciparum in Two Rural Cohort Populations in the Peruvian Amazon. J Infect Dis 2020; 223:1466-1477. [PMID: 32822474 DOI: 10.1093/infdis/jiaa526] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 08/17/2020] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Malaria is highly heterogeneous: its changing malaria microepidemiology needs to be addressed to support malaria elimination efforts at the regional level. METHODS A 3-year, population-based cohort study in 2 settings in the Peruvian Amazon (Lupuna, Cahuide) followed participants by passive and active case detection from January 2013 to December 2015. Incidence and prevalence rates were estimated using microscopy and polymerase chain reaction (PCR). RESULTS Lupuna registered 1828 infections (1708 Plasmodium vivax, 120 Plasmodium falciparum; incidence was 80.7 infections/100 person-years (95% confidence interval [CI] , 77.1-84.5). Cahuide detected 1046 infections (1024 P vivax, 20 P falciparum, 2 mixed); incidence was 40.2 infections/100 person-years (95% CI, 37.9-42.7). Recurrent P vivax infections predominated onwards from 2013. According to PCR data, submicroscopic predominated over microscopic infections, especially in periods of low transmission. The integration of parasitological, entomological, and environmental observations evidenced an intense and seasonal transmission resilient to standard control measures in Lupuna and a persistent residual transmission after severe outbreaks were intensively handled in Cahuide. CONCLUSIONS In 2 exemplars of complex local malaria transmission, standard control strategies failed to eliminate submicroscopic and hypnozoite reservoirs, enabling persistent transmission.
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Affiliation(s)
- Angel Rosas-Aguirre
- Research Institute of Health and Society, Université Catholique de Louvain, Brussels, Belgium.,Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Mitchel Guzman-Guzman
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Perú.,Laboratorio International Centers of Excellence in Malaria Research-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Raul Chuquiyauri
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Perú.,Laboratorio International Centers of Excellence in Malaria Research-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Marta Moreno
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, La Jolla, California, USA.,London School of Hygiene and Tropical Medicine, Department of Immunology and Infection, London, United Kingdom
| | - Paulo Manrique
- Laboratorio International Centers of Excellence in Malaria Research-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Roberson Ramirez
- Laboratorio International Centers of Excellence in Malaria Research-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Gabriel Carrasco-Escobar
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Perú.,Laboratorio International Centers of Excellence in Malaria Research-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú.,Division of Infectious Diseases, Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Hugo Rodriguez
- Dirección Regional de Salud Loreto DIRESA Loreto, Loreto, Perú
| | - Niko Speybroeck
- Research Institute of Health and Society, Université Catholique de Louvain, Brussels, Belgium
| | - Jan E Conn
- Wadsworth Center, New York State Department of Health, Albany, New York, USA.,Department of Biomedical Sciences, School of Public Health, University at Albany, State University of New York, Albany, New York, USA
| | - Dionicia Gamboa
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Perú.,Laboratorio International Centers of Excellence in Malaria Research-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú.,Departamento de Ciencias Celulares y Moleculares, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Joseph M Vinetz
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Perú.,Laboratorio International Centers of Excellence in Malaria Research-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú.,Departamento de Ciencias Celulares y Moleculares, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú.,Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Alejandro Llanos-Cuentas
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Perú.,Facultad de Salud Pública y Administración, Universidad Peruana Cayetano Heredia, Lima, Perú
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24
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Li Y, Hu Y, Zhao Y, Wang Q, Ngassa Mbenda HG, Kittichai V, Lawpoolsri S, Sattabongkot J, Menezes L, Liu X, Cui L, Cao Y. Dynamics of Plasmodium vivax populations in border areas of the Greater Mekong sub-region during malaria elimination. Malar J 2020; 19:145. [PMID: 32268906 PMCID: PMC7140319 DOI: 10.1186/s12936-020-03221-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 04/03/2020] [Indexed: 12/18/2022] Open
Abstract
Background Countries within the Greater Mekong Sub-region (GMS) of Southeast Asia have committed to eliminating malaria by 2030. Although the malaria situation has greatly improved, malaria transmission remains at international border regions. In some areas, Plasmodium vivax has become the predominant parasite. To gain a better understanding of transmission dynamics, knowledge on the changes of P. vivax populations after the scale-up of control interventions will guide more effective targeted control efforts. Methods This study investigated genetic diversity and population structures in 206 P. vivax clinical samples collected at two time points in two international border areas: the China-Myanmar border (CMB) (n = 50 in 2004 and n = 52 in 2016) and Thailand-Myanmar border (TMB) (n = 50 in 2012 and n = 54 in 2015). Parasites were genotyped using 10 microsatellite markers. Results Despite intensified control efforts, genetic diversity remained high (HE = 0.66–0.86) and was not significantly different among the four populations (P > 0.05). Specifically, HE slightly decreased from 0.76 in 2004 to 0.66 in 2016 at the CMB and increased from 0.80 in 2012 to 0.86 in 2015 at the TMB. The proportions of polyclonal infections varied significantly among the four populations (P < 0.05), and showed substantial decreases from 48.0% in 2004 to 23.7 at the CMB and from 40.0% in 2012 to 30.7% in 2015 at the TMB, with corresponding decreases in the multiplicity of infection. Consistent with the continuous decline of malaria incidence in the GMS over time, there were also increases in multilocus linkage disequilibrium, suggesting more fragmented and increasingly inbred parasite populations. There were considerable genetic differentiation and sub-division among the four tested populations. Temporal genetic differentiation was observed at each site (FST = 0.081 at the CMB and FST = 0.133 at the TMB). Various degrees of clustering were evident between the older parasite samples collected in 2004 at the CMB and the 2016 CMB and 2012 TMB populations, suggesting some of these parasites had shared ancestry. In contrast, the 2015 TMB population was genetically distinctive, which may reflect a process of population replacement. Whereas the effective population size (Ne) at the CMB showed a decrease from 4979 in 2004 to 3052 in 2016 with the infinite allele model, the Ne at the TMB experienced an increase from 6289 to 10,259. Conclusions With enhanced control efforts on malaria, P. vivax at the TMB and CMB showed considerable spatial and temporal differentiation, but the presence of large P. vivax reservoirs still sustained genetic diversity and transmission. These findings provide new insights into P. vivax transmission dynamics and population structure in these border areas of the GMS. Coordinated and integrated control efforts on both sides of international borders are essential to reach the goal of regional malaria elimination.
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Affiliation(s)
- Yuling Li
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, 110122, Liaoning, China.,Emergency Department, The First Affiliated Hospital of Dalian Medical University, Dalian, 116011, Liaoning, China
| | - Yubing Hu
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, 110122, Liaoning, China
| | - Yan Zhao
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, 110122, Liaoning, China
| | - Qinghui Wang
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, 110122, Liaoning, China
| | - Huguette Gaelle Ngassa Mbenda
- Division of Infectious Diseases and International Medicine, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Veerayuth Kittichai
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Saranath Lawpoolsri
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Jetsumon Sattabongkot
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Lynette Menezes
- Division of Infectious Diseases and International Medicine, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Xiaoming Liu
- Center for Global Health and Infectious Disease Research, College of Public Health, University of South Florida, Tampa, FL, 33612, USA
| | - Liwang Cui
- Division of Infectious Diseases and International Medicine, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA. .,Center for Global Health and Infectious Disease Research, College of Public Health, University of South Florida, Tampa, FL, 33612, USA.
| | - Yaming Cao
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, 110122, Liaoning, China.
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25
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Manrique P, Miranda-Alban J, Alarcon-Baldeon J, Ramirez R, Carrasco-Escobar G, Herrera H, Guzman-Guzman M, Rosas-Aguirre A, Llanos-Cuentas A, Vinetz JM, Escalante AA, Gamboa D. Microsatellite analysis reveals connectivity among geographically distant transmission zones of Plasmodium vivax in the Peruvian Amazon: A critical barrier to regional malaria elimination. PLoS Negl Trop Dis 2019; 13:e0007876. [PMID: 31710604 PMCID: PMC6874088 DOI: 10.1371/journal.pntd.0007876] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 11/21/2019] [Accepted: 10/25/2019] [Indexed: 12/31/2022] Open
Abstract
Despite efforts made over decades by the Peruvian government to eliminate malaria, Plasmodium vivax remains a challenge for public health decision-makers in the country. The uneven distribution of its incidence, plus its complex pattern of dispersion, has made ineffective control measures based on global information that lack the necessary detail to understand transmission fully. In this sense, population genetic tools can complement current surveillance. This study describes the genetic diversity and population structure from September 2012 to March 2015 in three geographically distant settlements, Cahuide (CAH), Lupuna (LUP) and Santa Emilia (STE), located in the Peruvian Amazon. A total 777 P. vivax mono-infections, out of 3264, were genotyped. Among study areas, LUP showed 19.7% of polyclonal infections, and its genetic diversity (Hexp) was 0.544. Temporal analysis showed a significant increment of polyclonal infections and Hexp, and the introduction and persistence of a new parasite population since March 2013. In STE, 40.1% of infections were polyclonal, with Hexp = 0.596. The presence of four genetic clusters without signals of clonal expansion and infections with lower parasite densities compared against the other two areas were also found. At least four parasite populations were present in CAH in 2012, where, after June 2014, malaria cases decreased from 213 to 61, concomitant with a decrease in polyclonal infections (from 0.286 to 0.18), and expectedly variable Hexp. Strong signals of gene flow were present in the study areas and wide geographic distribution of highly diverse parasite populations were found. This study suggests that movement of malaria parasites by human reservoirs connects geographically distant malaria transmission areas in the Peruvian Amazon. The maintenance of high levels of parasite genetic diversity through human mobility is a critical barrier to malaria elimination in this region. Plasmodium vivax transmission is heterogeneous and discontinuous in the Peruvian Amazon. Such heterogeneity is the result of factors that include, but are not restricted to, the environment, public policies, and characteristics of the parasite, the vector, and human activities. All these factors make P. vivax transmission resilient to interventions. In order to achieve the goals of control and local elimination, P. vivax surveillance must inform how those factors sustain disease transmission in order to focalize and synchronize control strategies. In this study, we implemented molecular surveillance complemented with population genetic tools in the areas of Cahuide, Lupuna, and Santa Emilia located in the Peruvian Amazon. In particular, we characterize the transmission and the parasite genetic variation in these sites from September 2012 to March 2015. The changes in parasite diversity, the wide geographic dispersion of parasite subpopulation and the introduction of a new parasite clone or subpopulation in Lupuna documented in this study suggest that connectivity among the different endemic areas, likely due to human mobility, sustains disease transmission in the region hindering the success of control measures. This information must be considered in the design of current control strategies.
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Affiliation(s)
- Paulo Manrique
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofa, Universidad Peruana Cayetano Heredia, Lima, Perú
- * E-mail:
| | - Julio Miranda-Alban
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofa, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Jhonatan Alarcon-Baldeon
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofa, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Roberson Ramirez
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofa, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Gabriel Carrasco-Escobar
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofa, Universidad Peruana Cayetano Heredia, Lima, Perú
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Henry Herrera
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofa, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Mitchel Guzman-Guzman
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofa, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Angel Rosas-Aguirre
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Perú
- Fund for Scientific Research FNRS, Brussels, Belgium
- Research Institute of Health and Society (IRSS), Université catholique de Louvain, Brussels, Belgium
| | - Alejandro Llanos-Cuentas
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Perú
- Facultad de Salud Pública y Administración, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Joseph M. Vinetz
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofa, Universidad Peruana Cayetano Heredia, Lima, Perú
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Perú
- Yale School of Medicine, Section of Infectious Diseases, Department of Internal Medicine, New Haven, Connecticut, United States of America
- Departamento de Ciencias Celulares y Moleculares, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Ananias A. Escalante
- Institute for Genomics and Evolutionary Medicine (IGEM), Temple University, Philadelphia, Pennsylvania, United States of America
| | - Dionicia Gamboa
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofa, Universidad Peruana Cayetano Heredia, Lima, Perú
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Perú
- Departamento de Ciencias Celulares y Moleculares, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
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26
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Miles LS, Rivkin LR, Johnson MTJ, Munshi‐South J, Verrelli BC. Gene flow and genetic drift in urban environments. Mol Ecol 2019; 28:4138-4151. [DOI: 10.1111/mec.15221] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 08/02/2019] [Accepted: 08/13/2019] [Indexed: 01/02/2023]
Affiliation(s)
- Lindsay S. Miles
- Integrative Life Sciences Doctoral Program Virginia Commonwealth University Richmond VA USA
- Department of Biology University of Toronto Mississauga Mississauga ON Canada
| | - L. Ruth Rivkin
- Department of Biology University of Toronto Mississauga Mississauga ON Canada
- Centre for Urban Environments University of Toronto Mississauga Mississauga ON Canada
- Department of Ecology and Evolutionary Biology University of Toronto Toronto ON Canada
| | - Marc T. J. Johnson
- Department of Biology University of Toronto Mississauga Mississauga ON Canada
- Centre for Urban Environments University of Toronto Mississauga Mississauga ON Canada
| | - Jason Munshi‐South
- Louis Calder Center—Biological Field Station Fordham University Armonk NY USA
| | - Brian C. Verrelli
- Center for Life Sciences Education Virginia Commonwealth University Richmond VA USA
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27
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Pacheco MA, Schneider KA, Céspedes N, Herrera S, Arévalo-Herrera M, Escalante AA. Limited differentiation among Plasmodium vivax populations from the northwest and to the south Pacific Coast of Colombia: A malaria corridor? PLoS Negl Trop Dis 2019; 13:e0007310. [PMID: 30921317 PMCID: PMC6456216 DOI: 10.1371/journal.pntd.0007310] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 04/09/2019] [Accepted: 03/16/2019] [Indexed: 01/06/2023] Open
Abstract
Background Malaria remains endemic in several countries of South America with low to moderate transmission intensity. Regional human migration through underserved endemic areas may be responsible for significant parasite dispersion making the disease resilient to interventions. Thus, the genetic characterization of malarial parasites is an important tool to assess how endemic areas may connect via the movement of infected individuals. Here, four sites in geographically separated areas reporting 80% of the malaria morbidity in Colombia were studied. The sites are located on an imaginary transect line of 1,500 km from the northwest to the south Pacific Coast of Colombia with a minimal distance of 500 km between populations that display noticeable ethnic, economic, epidemiological, and ecological differences. Methodology/Principal findings A total of 624 Plasmodium vivax samples from the four populations were genotyped by using eight microsatellite loci. Although a strong geographic structure was expected between these populations, only moderate evidence of genetic differentiation was observed using a suite of population genetic analyses. High genetic diversity, shared alleles, and low linkage disequilibrium were also found in these P. vivax populations providing no evidence for a bottleneck or clonal expansions as expected from recent reductions in the transmission that could have been the result of scaling up interventions or environmental changes. These patterns are consistent with a disease that is not only endemic in each site but also imply that there is gene flow among these populations across 1,500 km. Conclusion /Significance The observed patterns in P. vivax are consistent with a “corridor” where connected endemic areas can sustain a high level of genetic diversity locally and can restore parasite-subdivided populations via migration of infected individuals even after local interventions achieved a substantial reduction of clinical cases. The consequences of these findings in terms of control and elimination are discussed. The regional movements of infected individuals that connect suitable transmission areas make malaria resilient to control efforts. Those movements are expected to leave genetic signatures in the parasite populations that can be detected using analytical tools. In this study, the genetic makeups of Plasmodium vivax populations were characterized to assess whether the most endemic areas in Colombia were connected. Samples were collected from passive surveillance studies in four locations across an imaginary transect line of 1,500 km from the northwest to the south Pacific Coast of Colombia (South America). Considering the distance, and contrary to expectations, we found weak levels of genetic differentiation between these parasite populations with no evidence indicating that their genetic diversity has been eroded as expected whenever the prevalence of the disease is successfully reduced, e.g., through control programs or environmental changes. Although the sampling lacks the geographic and temporal detail to describe how the dispersion of parasite lineages occurred, the observed patterns are consistent with a series of infected populations that are connected in space by human movements allowing the parasite to diffuse across this 1,500 km transect. This malaria corridor needs to be characterized to achieve elimination.
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Affiliation(s)
- M. Andreína Pacheco
- Department of Biology/Institute for Genomics and Evolutionary Medicine (iGEM), Temple University, Philadelphia, Pennsylvania, United States of America
| | | | - Nora Céspedes
- Caucaseco Scientific Research Center and Malaria Vaccine and Drug Development Center, Cali, Colombia
| | - Sócrates Herrera
- Caucaseco Scientific Research Center and Malaria Vaccine and Drug Development Center, Cali, Colombia
| | - Myriam Arévalo-Herrera
- Caucaseco Scientific Research Center and Malaria Vaccine and Drug Development Center, Cali, Colombia
- Faculty of Health, Universidad del Valle, Cali, Colombia
| | - Ananias A. Escalante
- Department of Biology/Institute for Genomics and Evolutionary Medicine (iGEM), Temple University, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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28
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Carrasco-Escobar G, Castro MC, Barboza JL, Ruiz-Cabrejos J, Llanos-Cuentas A, Vinetz JM, Gamboa D. Use of open mobile mapping tool to assess human mobility traceability in rural offline populations with contrasting malaria dynamics. PeerJ 2019; 7:e6298. [PMID: 30697487 PMCID: PMC6346981 DOI: 10.7717/peerj.6298] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 12/18/2018] [Indexed: 11/20/2022] Open
Abstract
Infectious disease dynamics are affected by human mobility more powerfully than previously thought, and thus reliable traceability data are essential. In rural riverine settings, lack of infrastructure and dense tree coverage deter the implementation of cutting-edge technology to collect human mobility data. To overcome this challenge, this study proposed the use of a novel open mobile mapping tool, GeoODK. This study consists of a purposive sampling of 33 participants in six villages with contrasting patterns of malaria transmission that demonstrates a feasible approach to map human mobility. The self-reported traceability data allowed the construction of the first human mobility framework in rural riverine villages in the Peruvian Amazon. The mobility spectrum in these areas resulted in travel profiles ranging from 2 hours to 19 days; and distances between 10 to 167 km. Most Importantly, occupational-related mobility profiles with the highest displacements (in terms of time and distance) were observed in commercial, logging, and hunting activities. These data are consistent with malaria transmission studies in the area that show villages in watersheds with higher human movement are concurrently those with greater malaria risk. The approach we describe represents a potential tool to gather critical information that can facilitate malaria control activities.
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Affiliation(s)
- Gabriel Carrasco-Escobar
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru.,Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA, United States of America
| | - Marcia C Castro
- Department of Global Health and Population, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
| | - Jose Luis Barboza
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Jorge Ruiz-Cabrejos
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Alejandro Llanos-Cuentas
- Instituto de Medicinal Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Joseph M Vinetz
- Instituto de Medicinal Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru.,Department of Infectious diseases, School of Medicine, Yale University, New Haven, CT, United States of America
| | - Dionicia Gamboa
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru.,Instituto de Medicinal Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru.,Departamento de Ciencias Celulares y Moleculares, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
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Nkhoma SC, Banda RL, Khoswe S, Dzoole-Mwale TJ, Ward SA. Intra-host dynamics of co-infecting parasite genotypes in asymptomatic malaria patients. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2018; 65:414-424. [PMID: 30145390 PMCID: PMC6219893 DOI: 10.1016/j.meegid.2018.08.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 08/13/2018] [Accepted: 08/20/2018] [Indexed: 11/22/2022]
Abstract
Malaria-infected individuals often harbor mixtures of genetically distinct parasite genotypes. We studied intra-host dynamics of parasite genotypes co-infecting asymptomatic adults in an area of intense malaria transmission in Chikhwawa, Malawi. Serial blood samples (5 ml) were collected over seven consecutive days from 25 adults with asymptomatic Plasmodium falciparum malaria and analyzed to determine whether a single peripheral blood sample accurately captures within-host parasite diversity. Blood samples from three of the participants were also analyzed by limiting dilution cloning and SNP genotyping of the parasite clones isolated to examine both the number and relatedness of co-infecting parasite haplotypes. We observed rapid turnover of co-infecting parasite genotypes in 88% of the individuals sampled (n = 22) such that the genetic composition of parasites infecting these individuals changed dramatically over the course of seven days of follow up. Nineteen of the 25 individuals sampled (76%) carried multiple parasite genotypes at baseline. Analysis of serial blood samples from three of the individuals revealed that they harbored 6, 12 and 17 distinct parasite haplotypes respectively. Approximately 70% of parasite haplotypes recovered from the three extensively sampled individuals were unrelated (proportion of shared alleles <83.3%) and were deemed to have primarily arisen from superinfection (inoculation of unrelated parasite haplotypes through multiple mosquito bites). The rest were related at the half-sib level or greater and were deemed to have been inoculated into individual human hosts via parasite co-transmission from single mosquito bites. These findings add further to the growing weight of evidence indicating that a single blood sample poorly captures within-host parasite diversity and underscore the importance of repeated blood sampling to accurately capture within-host parasite ecology. Our data also demonstrate a more pronounced role for parasite co-transmission in generating within-host parasite diversity in high transmission settings than previously assumed. Taken together, these findings have important implications for understanding the evolution of drug resistance, malaria transmission, parasite virulence, allocation of gametocyte sex ratios and acquisition of malaria immunity.
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Affiliation(s)
- Standwell C Nkhoma
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi; Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK; Wellcome Trust-Liverpool-Glasgow Centre for Global Health Research, 70 Pembroke Place, Liverpool L69 3GF, UK.
| | - Rachel L Banda
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Stanley Khoswe
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Tamika J Dzoole-Mwale
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Stephen A Ward
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
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30
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Cowell AN, Valdivia HO, Bishop DK, Winzeler EA. Exploration of Plasmodium vivax transmission dynamics and recurrent infections in the Peruvian Amazon using whole genome sequencing. Genome Med 2018; 10:52. [PMID: 29973248 PMCID: PMC6032790 DOI: 10.1186/s13073-018-0563-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 06/25/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Plasmodium vivax poses a significant challenge to malaria elimination due to its ability to cause relapsed infections from reactivation of dormant liver parasites called hypnozoites. We analyzed 69 P. vivax whole genome sequences obtained from subjects residing in three different villages along the Peruvian Amazon. This included 23 paired P. vivax samples from subjects who experienced recurrent P. vivax parasitemia following observed treatment with chloroquine and primaquine. METHODS Genomic DNA was extracted from whole blood samples collected from subjects. P. vivax DNA was enriched using selective whole genome amplification and whole genome sequencing. We used single nucleotide polymorphisms (SNPs) from the core P. vivax genome to determine characteristics of the parasite population using discriminant analysis of principal components, maximum likelihood estimation of individual ancestries, and phylogenetic analysis. We estimated the relatedness of the paired samples by calculating the number of segregating sites and using a hidden Markov model approach to estimate identity by descent. RESULTS We present a comprehensive dataset of population genetics of Plasmodium vivax in the Peruvian Amazonian. We define the parasite population structure in this region and demonstrate a novel method for distinguishing homologous relapses from reinfections or heterologous relapses with improved accuracy. The parasite population in this area was quite diverse with an estimated five subpopulations and evidence of a highly heterogeneous ancestry of some of the isolates, similar to previous analyses of P. vivax in this region. Pairwise comparison of recurrent infections determined that there were 12 homologous relapses and 3 likely heterologous relapses with highly related parasites. To the best of our knowledge, this is the first large-scale study to evaluate recurrent P. vivax infections using whole genome sequencing. CONCLUSIONS Whole genome sequencing is a high-resolution tool that can identify P. vivax homologous relapses with increased sensitivity, while also providing data about drug resistance and parasite population genetics. This information is important for evaluating the efficacy of known and novel antirelapse medications in endemic areas and thus advancing the campaign to eliminate malaria.
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Affiliation(s)
- Annie N Cowell
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA.
| | - Hugo O Valdivia
- U.S. Naval Medical Research No. 6, Venezuela Ave, Block 36, Bellavista, Callao, Peru
| | - Danett K Bishop
- U.S. Naval Medical Research No. 6, Venezuela Ave, Block 36, Bellavista, Callao, Peru
| | - Elizabeth A Winzeler
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, UC San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
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Ventocilla JA, Nuñez J, Tapia LL, Lucas CM, Manock SR, Lescano AG, Edgel KA, Graf PCF. Genetic Variability of Plasmodium vivax in the North Coast of Peru and the Ecuadorian Amazon Basin. Am J Trop Med Hyg 2018; 99:27-32. [PMID: 29761758 DOI: 10.4269/ajtmh.17-0498] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
In the Peruvian North Coast (PNC), the number of Plasmodium vivax malaria cases increased steadily from 2007 to 2010 despite a significant decline in the overall number of cases in Peru during the same period. To better understand the transmission dynamics of P. vivax populations in the PNC and the neighboring Ecuadorian Amazon Basin (EAB), we studied the genetic variability and population structure of P. vivax in these areas. One hundred and twenty P. vivax isolates (58 from Piura and 37 from Tumbes in the PNC collected from 2008 to 2010 and 25 from the EAB collected in Pastaza from 2001 to 2004) were assessed by five polymorphic microsatellite markers. Genetic variability was determined by expected heterozygosity (He) and population structure by Bayesian inference cluster analysis. We found very low genetic diversity in the PNC (He = 0-0.32) but high genetic diversity in the EAB (He = 0.43-0.70). Population structure analysis revealed three distinct populations in the three locations. Six of 37 (16%) isolates from Tumbes had an identical haplotype to that found in Piura, suggesting unidirectional flow from Piura to Tumbes. In addition, one haplotype from Tumbes showed similarity to a haplotype found in Pastaza, suggesting that this could be an imported case from EAB. These findings strongly suggest a minimal population flow and different levels of genetic variability between these two areas divided by the Andes Mountains. This work presents molecular markers that could be used to increase our understanding of regional malaria transmission dynamics, which has implications for the development of strategies for P. vivax control.
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Affiliation(s)
| | - Jorge Nuñez
- U.S. Naval Medical Research Unit 6 (NAMRU-6), Lima, Peru
| | - L Lorena Tapia
- U.S. Naval Medical Research Unit 6 (NAMRU-6), Lima, Peru
| | - Carmen M Lucas
- U.S. Naval Medical Research Unit 6 (NAMRU-6), Lima, Peru
| | | | - Andrés G Lescano
- Emerge, Emerging Diseases and Climate Change Research Unit, School of Public Health and Administration Universidad Peruana Cayetano Heredia, Lima, Peru.,U.S. Naval Medical Research Unit 6 (NAMRU-6), Lima, Peru
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Zhong D, Koepfli C, Cui L, Yan G. Molecular approaches to determine the multiplicity of Plasmodium infections. Malar J 2018; 17:172. [PMID: 29685152 PMCID: PMC5914063 DOI: 10.1186/s12936-018-2322-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 04/18/2018] [Indexed: 12/26/2022] Open
Abstract
Multiplicity of infection (MOI), also termed complexity of infection (COI), is defined as the number of genetically distinct parasite strains co-infecting a single host, which is an important indicator of malaria epidemiology. PCR-based genotyping often underestimates MOI. Next generation sequencing technologies provide much more accurate and genome-wide characterization of polyclonal infections. However, complete haplotype characterization of multiclonal infections remains a challenge due to PCR artifacts and sequencing errors, and requires efficient computational tools. In this review, the advantages and limitations of current molecular approaches to determine multiplicity of malaria parasite infection are discussed.
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Affiliation(s)
- Daibin Zhong
- Program in Public Health, University of California, Irvine, CA, 92617, USA.
| | - Cristian Koepfli
- Program in Public Health, University of California, Irvine, CA, 92617, USA
| | - Liwang Cui
- Department of Entomology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Guiyun Yan
- Program in Public Health, University of California, Irvine, CA, 92617, USA.
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Abstract
Our planet is an increasingly urbanized landscape, with over half of the human population residing in cities. Despite advances in urban ecology, we do not adequately understand how urbanization affects the evolution of organisms, nor how this evolution may affect ecosystems and human health. Here, we review evidence for the effects of urbanization on the evolution of microbes, plants, and animals that inhabit cities. Urbanization affects adaptive and nonadaptive evolutionary processes that shape the genetic diversity within and between populations. Rapid adaptation has facilitated the success of some native species in urban areas, but it has also allowed human pests and disease to spread more rapidly. The nascent field of urban evolution brings together efforts to understand evolution in response to environmental change while developing new hypotheses concerning adaptation to urban infrastructure and human socioeconomic activity. The next generation of research on urban evolution will provide critical insight into the importance of evolution for sustainable interactions between humans and our city environments.
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Affiliation(s)
- Marc T J Johnson
- Department of Biology and Center for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada. .,Department of Ecology and Evolutionary Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Jason Munshi-South
- Department of Biological Sciences and Louis Calder Center, Fordham University, Armonk, NY, USA.
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Increasingly inbred and fragmented populations of Plasmodium vivax associated with the eastward decline in malaria transmission across the Southwest Pacific. PLoS Negl Trop Dis 2018; 12:e0006146. [PMID: 29373596 PMCID: PMC5802943 DOI: 10.1371/journal.pntd.0006146] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 02/07/2018] [Accepted: 12/01/2017] [Indexed: 01/17/2023] Open
Abstract
The human malaria parasite Plasmodium vivax is more resistant to malaria control strategies than Plasmodium falciparum, and maintains high genetic diversity even when transmission is low. To investigate whether declining P. vivax transmission leads to increasing population structure that would facilitate elimination, we genotyped samples from across the Southwest Pacific region, which experiences an eastward decline in malaria transmission, as well as samples from two time points at one site (Tetere, Solomon Islands) during intensified malaria control. Analysis of 887 P. vivax microsatellite haplotypes from hyperendemic Papua New Guinea (PNG, n = 443), meso-hyperendemic Solomon Islands (n = 420), and hypoendemic Vanuatu (n = 24) revealed increasing population structure and multilocus linkage disequilibrium yet a modest decline in diversity as transmission decreases over space and time. In Solomon Islands, which has had sustained control efforts for 20 years, and Vanuatu, which has experienced sustained low transmission for many years, significant population structure was observed at different spatial scales. We conclude that control efforts will eventually impact P. vivax population structure and with sustained pressure, populations may eventually fragment into a limited number of clustered foci that could be targeted for elimination. Plasmodium vivax is a major human malaria parasite, common in endemic areas outside sub-Saharan Africa, and more difficult to control than other malaria parasite species. The distinct lifecycle biology of P. vivax is thought to contribute to its more stable and efficient transmission allowing the maintenance of high diversity and potentially, gene flow. Independent studies are therefore needed to understand how P. vivax populations respond to changing transmission levels, in order to inform malaria control and elimination efforts. Here we have determined parasite population genetic structure in three countries of the Southwest Pacific, an island chain with a natural west to east decline in transmission intensity (Papua New Guinea > Solomon Islands > Vanuatu). With declining transmission, P. vivax populations experience only a modest decline in diversity but a significant increase in multilocus linkage disequilibrium and population structure, indicating that parasite populations become more inbred and begin to fragment into clustered foci. Analysis of two time points in one study area (Tetere, Solomon Islands) also show similar changes in association with intensifying malaria control. The results indicate that with long term sustained malaria control P. vivax populations will eventually fracture into population clusters that could be targeted for elimination.
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Carrasco-Escobar G, Miranda-Alban J, Fernandez-Miñope C, Brouwer KC, Torres K, Calderon M, Gamboa D, Llanos-Cuentas A, Vinetz JM. High prevalence of very-low Plasmodium falciparum and Plasmodium vivax parasitaemia carriers in the Peruvian Amazon: insights into local and occupational mobility-related transmission. Malar J 2017; 16:415. [PMID: 29037202 PMCID: PMC5644076 DOI: 10.1186/s12936-017-2063-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/11/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The incidence of malaria due both to Plasmodium falciparum and Plasmodium vivax in the Peruvian Amazon has risen in the past 5 years. This study tested the hypothesis that the maintenance and emergence of malaria in hypoendemic regions such as Amazonia is determined by submicroscopic and asymptomatic Plasmodium parasitaemia carriers. The present study aimed to precisely quantify the rate of very-low parasitaemia carriers in two sites of the Peruvian Amazon in relation to transmission patterns of P. vivax and P. falciparum in this area. METHODS This study was carried out within the Amazonian-ICEMR longitudinal cohort. Blood samples were collected for light microscopy diagnosis and packed red blood cell (PRBC) samples were analysed by qPCR. Plasma samples were tested for total IgG reactivity against recombinant PvMSP-10 and PfMSP-10 antigens by ELISA. Occupation and age 10 years and greater were considered surrogates of occupation-related mobility. Risk factors for P. falciparum and P. vivax infections detected by PRBC-qPCR were assessed by multilevel logistic regression models. RESULTS Among 450 subjects, the prevalence of P. vivax by PRBC-PCR (25.1%) was sixfold higher than that determined by microscopy (3.6%). The prevalence of P. falciparum infection was 4.9% by PRBC-PCR and 0.2% by microscopy. More than 40% of infections had parasitaemia under 5 parasites/μL. Multivariate analysis for infections detected by PRBC-PCR showed that participants with recent settlement in the study area (AOR 2.1; 95% CI 1.03:4.2), age ≥ 30 years (AOR 3.3; 95% CI 1.6:6.9) and seropositivity to P. vivax (AOR 1.8; 95% CI 1.0:3.2) had significantly higher likelihood of P. vivax infection, while the odds of P. falciparum infection was higher for participants between 10 and 29 years (AOR 10.7; 95% CI 1.3:91.1) and with a previous P. falciparum infection (AOR 10.4; 95% CI 1.5:71.1). CONCLUSIONS This study confirms the contrasting transmission patterns of P. vivax and P. falciparum in the Peruvian Amazon, with stable local transmission for P. vivax and the source of P. falciparum to the study villages dominated by very low parasitaemia carriers, age 10 years and older, who had travelled away from home for work and brought P. falciparum infection with them.
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Affiliation(s)
- Gabriel Carrasco-Escobar
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
- Facultad de Salud Pública, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Julio Miranda-Alban
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Carlos Fernandez-Miñope
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Kimberly C. Brouwer
- Division of Epidemiology, Department of Family Medicine & Public Health, University of California, San Diego, La Jolla, CA USA
| | - Katherine Torres
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
- Departamento de Ciencias Celulares y Moleculares, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Maritza Calderon
- Departamento de Ciencias Celulares y Moleculares, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Dionicia Gamboa
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
- Departamento de Ciencias Celulares y Moleculares, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
- Instituto de Medicinal Tropical “Alexander von Humboldt”, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Alejandro Llanos-Cuentas
- Facultad de Salud Pública, Universidad Peruana Cayetano Heredia, Lima, Peru
- Instituto de Medicinal Tropical “Alexander von Humboldt”, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Joseph M. Vinetz
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
- Departamento de Ciencias Celulares y Moleculares, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
- Instituto de Medicinal Tropical “Alexander von Humboldt”, Universidad Peruana Cayetano Heredia, Lima, Peru
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, 9500 Gilman Drive MC0760, Biomedical Research Facility-2, Room 4A16, La Jolla, CA USA
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Abstract
Plasmodium vivax is the second most prevalent cause of malaria worldwide and the leading cause of malaria outside of Africa. Although infections are seldom fatal clinical disease can be debilitating and imposes significant health and economic impacts on affected populations. Estimates of transmission and prevalence intensity can be problematic because many episodes of vivax originate from hypnozoite stages in the liver that have remained dormant from previous infections by an unknown mechanism. Lack of treatment options to clear hypnozoites and the ability to infect mosquitoes before disease symptoms present represent major challenges for control and eradication of vivax malaria. Compounding these challenges is the unique biology of P. vivax and limited progress in development of experimental research tools, thereby hindering development of new drugs and vaccines. Renewed emphasis on vivax malaria research is beginning to make progress in overcoming some of these challenges.
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Affiliation(s)
- John H Adams
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, Tampa, Florida 33612
| | - Ivo Mueller
- Population Health & Immunity Division, Walter & Eliza Hall Institute, Parkville, Victoria 3052, Australia
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37
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Carrasco-Escobar G, Gamboa D, Castro MC, Bangdiwala SI, Rodriguez H, Contreras-Mancilla J, Alava F, Speybroeck N, Lescano AG, Vinetz JM, Rosas-Aguirre A, Llanos-Cuentas A. Micro-epidemiology and spatial heterogeneity of P. vivax parasitaemia in riverine communities of the Peruvian Amazon: A multilevel analysis. Sci Rep 2017; 7:8082. [PMID: 28808240 PMCID: PMC5556029 DOI: 10.1038/s41598-017-07818-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 07/04/2017] [Indexed: 01/07/2023] Open
Abstract
Malaria has steadily increased in the Peruvian Amazon over the last five years. This study aimed to determine the parasite prevalence and micro-geographical heterogeneity of Plasmodium vivax parasitaemia in communities of the Peruvian Amazon. Four cross-sectional active case detection surveys were conducted between May and July 2015 in four riverine communities in Mazan district. Analysis of 2785 samples of 820 individuals nested within 154 households for Plasmodium parasitaemia was carried out using light microscopy and qPCR. The spatio-temporal distribution of Plasmodium parasitaemia, dominated by P. vivax, was shown to cluster at both household and community levels. Of enrolled individuals, 47% had at least one P. vivax parasitaemia and 10% P. falciparum, by qPCR, both of which were predominantly sub-microscopic and asymptomatic. Spatial analysis detected significant clustering in three communities. Our findings showed that communities at small-to-moderate spatial scales differed in P. vivax parasite prevalence, and multilevel Poisson regression models showed that such differences were influenced by factors such as age, education, and location of households within high-risk clusters, as well as factors linked to a local micro-geographic context, such as travel and occupation. Complex transmission patterns were found to be related to human mobility among communities in the same micro-basin.
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Affiliation(s)
- Gabriel Carrasco-Escobar
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigacióny Desarrollo, Facultad de Cienciasy Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru.
- Facultad de Salud Públicay Administración, Universidad Peruana Cayetano Heredia, Lima, Peru.
| | - Dionicia Gamboa
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigacióny Desarrollo, Facultad de Cienciasy Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
- Instituto de Medicina Tropical "Alexander von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru
- Departamento de Ciencias Celularesy Moleculares, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Marcia C Castro
- Department of Global Health and Population, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Shrikant I Bangdiwala
- Department of Biostatistics, University of North Carolina Gillings School of Global Public Health, Chapel Hill, NC, USA
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, ON, Canada
| | | | - Juan Contreras-Mancilla
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigacióny Desarrollo, Facultad de Cienciasy Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | - Niko Speybroeck
- Research Institute of Health and Society (IRSS), Université Catholique de Louvain, Brussels, Belgium
| | - Andres G Lescano
- Facultad de Salud Públicay Administración, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Joseph M Vinetz
- Instituto de Medicina Tropical "Alexander von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru
- Departamento de Ciencias Celularesy Moleculares, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
- Division of Infectious Diseases, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, USA
| | - Angel Rosas-Aguirre
- Instituto de Medicina Tropical "Alexander von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru
- Research Institute of Health and Society (IRSS), Université Catholique de Louvain, Brussels, Belgium
| | - Alejandro Llanos-Cuentas
- Facultad de Salud Públicay Administración, Universidad Peruana Cayetano Heredia, Lima, Peru.
- Instituto de Medicina Tropical "Alexander von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru.
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Rovira-Vallbona E, Contreras-Mancilla JJ, Ramirez R, Guzmán-Guzmán M, Carrasco-Escobar G, Llanos-Cuentas A, Vinetz JM, Gamboa D, Rosanas-Urgell A. Predominance of asymptomatic and sub-microscopic infections characterizes the Plasmodium gametocyte reservoir in the Peruvian Amazon. PLoS Negl Trop Dis 2017; 11:e0005674. [PMID: 28671944 PMCID: PMC5510906 DOI: 10.1371/journal.pntd.0005674] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 07/14/2017] [Accepted: 05/31/2017] [Indexed: 11/18/2022] Open
Abstract
Malaria transmission requires that Anopheles mosquitoes ingest Plasmodium gametocyte stages circulating in the human bloodstream. In the context of malaria elimination, understanding the epidemiology of gametocytes relative to all Plasmodium infections and the contribution of asymptomatic and sub-microscopic parasite carriers to the gametocyte reservoir is necessary, especially in low endemic settings with predominance of P.vivax. A 13-month longitudinal study was conducted in two communities (n = 1935 individuals) of Loreto Department, Peru, with five active screenings for Plasmodium infections and gametocyte stages by quantitative real-time PCR (qPCR) and reverse transcription (RT)-qPCR, respectively. Parasite prevalence by qPCR was 7.2% for P.vivax (n = 520/7235; range by survey 6.0%-8.1%) and 3.2% for P.falciparum (n = 235/7235; range by survey 0.4%-7.7%). Sub-microscopic infections accounted for 73.5% of P.vivax (range by survey 60%-89%) and almost the totality of P.falciparum cases. Gametocytes were found in 28.4% P.vivax infections (range by survey 18.7%-34.1%), with a peak of 61.5% in one community at the start of the transmission season. About 59.8% of all P.vivax gametocyte carriers were asymptomatic and 31.9% were sub-microscopic. Age patterns for gametocyte prevalence paralleled asexual stage infections and peaked among >15–25 year old individuals. Asexual parasite density was found to be the strongest predictor for P.vivax gametocyte presence in longitudinal multivariate analysis (odds ratio 2.33 [95% confidence interval 1.96, 2.78]; P<0.001). Despite significant differences in seasonality patterns and P.vivax prevalence found at the local scale, sub-microscopic and asymptomatic infections predominate and contribute significantly to the gametocyte reservoir in different communities of the Peruvian Amazon. Control and elimination campaigns need sensitive tools to detect all infections that escape routine malaria surveillance, which may contribute to maintain transmission in the region. Malaria elimination, i.e. the complete interruption of parasite transmission in a region, is in the agenda of health authorities in countries that achieved substantial reduction of the disease burden in the past decade. However, our understanding of transmission epidemiology for low transmission areas where Plasmodium vivax is endemic, like the Amazon basin, is still limited. In this study, we describe the prevalence and risk factors for carrying the parasite stages that are transmitted to the mosquito vectors, named gametocytes, in 1935 individuals from two communities of the Peruvian Amazon that were regularly screened during 1 year. We report that malaria infections with no clinical symptoms and those with parasite levels below microscopy detection threshold, account for two thirds of all P.vivax infections with gametocytes, and that the highest infection rate is found among young adults. In addition, almost the totality of P.falciparum infections detected was sub-microscopic. Because all these infections escape current malaria surveillance systems -based on passive case detection and/or microscopy diagnosis-, new approaches are necessary to target all infections in order to eliminate the malaria transmission reservoir in Peru.
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Affiliation(s)
- Eduard Rovira-Vallbona
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- * E-mail:
| | | | - Roberson Ramirez
- Laboratorio Satelite Iquitos UPCH-UCSD, Universidad Peruana Cayetano Heredia, Loreto, Peru
| | - Mitchel Guzmán-Guzmán
- Laboratorio Satelite Iquitos UPCH-UCSD, Universidad Peruana Cayetano Heredia, Loreto, Peru
| | - Gabriel Carrasco-Escobar
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Alejandro Llanos-Cuentas
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Joseph M. Vinetz
- Department of Medicine, University of California San Diego, San Diego, California, United States of America
| | - Dionicia Gamboa
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Departamento de Ciencias Celulares y Moleculares, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Anna Rosanas-Urgell
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
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Baraka V, Delgado-Ratto C, Nag S, Ishengoma DS, Madebe RA, Mavoko HM, Nabasumba C, Lutumba P, Alifrangis M, Van Geertruyden JP. Different origin and dispersal of sulfadoxine-resistant Plasmodium falciparum haplotypes between Eastern Africa and Democratic Republic of Congo. Int J Antimicrob Agents 2017; 49:456-464. [PMID: 28237831 DOI: 10.1016/j.ijantimicag.2016.12.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Revised: 12/05/2016] [Accepted: 12/17/2016] [Indexed: 10/20/2022]
Abstract
Sulfadoxine/pyrimethamine (SP) is still used for malaria control in sub-Saharan Africa; however, widespread resistance is a major concern. This study aimed to determine the dispersal and origin of sulfadoxine resistance lineages in the Democratic Republic of the Congo compared with East African Plasmodium falciparum dihydropteroate synthetase (Pfdhps) haplotypes. The analysis involved 264 isolates collected from patients with uncomplicated malaria from Tanzania, Uganda and DR Congo. Isolates were genotyped for Pfdhps mutations at codons 436, 437, 540, 581 and 613. Three microsatellite loci (0.8, 4.3 and 7.7 kb) flanking the Pfdhps gene were assayed. Evolutionary analysis revealed a shared origin of Pfdhps haplotypes in East Africa, with a distinct population clustering in DR Congo. Furthermore, in Tanzania there was an independent distinct origin of Pfdhps SGEGA resistant haplotype. In Uganda and Tanzania, gene flow patterns contribute to the dispersal and shared origin of parasites carrying double- and triple-mutant Pfdhps haplotypes associated with poor outcomes of intermittent preventive treatment during pregnancy using SP (IPTp-SP). However, the origins of the Pfdhps haplotypes in DR Congo and Eastern Africa sites are different. The genetic structure demonstrated a divergent and distinct population cluster predominated by single-mutant Pfdhps haplotypes at the DR Congo site. This reflects the limited dispersal of double- and triple-mutant Pfdhps haplotypes in DR Congo. This study highlights the current genetic structure and dispersal of high-grade Pfdhps resistant haplotypes, which is important to guide implementation of SP in malaria chemoprevention strategies in the region.
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Affiliation(s)
- Vito Baraka
- National Institute for Medical Research, Tanga Research Centre, P.O. Box 5004, Tanga, United Republic of Tanzania; Global Health Institute, University of Antwerp, Antwerp, Belgium.
| | | | - Sidsel Nag
- Centre for Medical Parasitology at the Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark; Department of Infectious Diseases, National University Hospital (Rigshospitalet), Copenhagen, Denmark
| | - Deus S Ishengoma
- National Institute for Medical Research, Tanga Research Centre, P.O. Box 5004, Tanga, United Republic of Tanzania
| | - Rashid A Madebe
- National Institute for Medical Research, Tanga Research Centre, P.O. Box 5004, Tanga, United Republic of Tanzania
| | - Hypolite Muhindo Mavoko
- Global Health Institute, University of Antwerp, Antwerp, Belgium; Département de Médecine Tropicale, Faculté de Médecine, Université de Kinshasa, B.P. 747 Kin XI, Kinshasa, The Democratic Republic of the Congo
| | - Carolyn Nabasumba
- Global Health Institute, University of Antwerp, Antwerp, Belgium; Epicentre Mbarara Research Base, P.O. Box 930, Mbarara, Uganda
| | - Pascal Lutumba
- Département de Médecine Tropicale, Faculté de Médecine, Université de Kinshasa, B.P. 747 Kin XI, Kinshasa, The Democratic Republic of the Congo
| | - Michael Alifrangis
- Centre for Medical Parasitology at the Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark; Department of Infectious Diseases, National University Hospital (Rigshospitalet), Copenhagen, Denmark
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40
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Auburn S, Barry AE. Dissecting malaria biology and epidemiology using population genetics and genomics. Int J Parasitol 2016; 47:77-85. [PMID: 27825828 DOI: 10.1016/j.ijpara.2016.08.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 08/09/2016] [Accepted: 08/25/2016] [Indexed: 10/20/2022]
Abstract
Molecular approaches have an increasingly recognized utility in surveillance of malaria parasite populations, not only in defining prevalence and incidence with higher sensitivity than traditional methods, but also in monitoring local and regional parasite transmission patterns. In this review, we provide an overview of population genetic and genomic studies of human-infecting Plasmodium species, highlighting recent advances in the field. In accordance with the renewed impetus for malaria eradication, many studies are now using genetic and genomic epidemiology to support local evidence-based intervention strategies. Microsatellite genotyping remains a popular approach for both Plasmodium falciparum and Plasmodium vivax. However, with the increasing availability of whole genome sequencing data enabling effective single nucleotide polymorphism-based panels tailored to a given study question and setting, this approach is gaining popularity. The availability of new reference genomes for Plasmodium malariae and Plasmodium ovale should see a surge in similar molecular studies on these currently neglected species. Genomic studies are revealing new insights into important adaptive mechanisms of the parasite including antimalarial drug resistance. The advent of new methodologies such as selective whole genome amplification for dealing with extensive human DNA in low density field isolates should see genome-wide approaches becoming routine for parasite surveillance once the economic costs outweigh the current cost benefits of targeted approaches.
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Affiliation(s)
- Sarah Auburn
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Australia
| | - Alyssa E Barry
- Division of Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; Department of Medical Biology, University of Melbourne, Melbourne, Australia.
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41
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Rosas-Aguirre A, Gamboa D, Manrique P, Conn JE, Moreno M, Lescano AG, Sanchez JF, Rodriguez H, Silva H, Llanos-Cuentas A, Vinetz JM. Epidemiology of Plasmodium vivax Malaria in Peru. Am J Trop Med Hyg 2016; 95:133-144. [PMID: 27799639 PMCID: PMC5201219 DOI: 10.4269/ajtmh.16-0268] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 09/29/2016] [Indexed: 01/01/2023] Open
Abstract
Malaria in Peru, dominated by Plasmodium vivax, remains a public health problem. The 1990s saw newly epidemic malaria emerge, primarily in the Loreto Department in the Amazon region, including areas near to Iquitos, the capital city, but sporadic malaria transmission also occurred in the 1990s–2000s in both north-coastal Peru and the gold mining regions of southeastern Peru. Although a Global Fund-supported intervention (PAMAFRO, 2005–2010) was temporally associated with a decrease of malaria transmission, from 2012 to the present, both P. vivax and Plasmodium falciparum malaria cases have rapidly increased. The Peruvian Ministry of Health continues to provide artemesinin-based combination therapy for microscopy-confirmed cases of P. falciparum and chloroquine–primaquine for P. vivax. Malaria transmission continues in remote areas nonetheless, where the mobility of humans and parasites facilitates continued reintroduction outside of ongoing surveillance activities, which is critical to address for future malaria control and elimination efforts. Ongoing P. vivax research gaps in Peru include the following: identification of asymptomatic parasitemics, quantification of the contribution of patent and subpatent parasitemics to mosquito transmission, diagnosis of nonparasitemic hypnozoite carriers, and implementation of surveillance for potential emergence of chloroquine- and 8-aminoquinoline-resistant P. vivax. Clinical trials of tafenoquine in Peru have been promising, and glucose-6-phosphate dehydrogenase deficiency in the region has not been observed to be a limitation to its use. Larger-scale challenges for P. vivax (and malaria in general) in Peru include logistical difficulties in accessing remote riverine populations, consequences of government policy and poverty trends, and obtaining international funding for malaria control and elimination.
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Affiliation(s)
- Angel Rosas-Aguirre
- Research Institute of Health and Society, Université Catholique de Louvain, Brussels, Belgium.,Instituto de Medicina Tropical "Alexander von Humboldt," Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Dionicia Gamboa
- Departamento de Ciencias Celulares y Moleculares, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru.,Instituto de Medicina Tropical "Alexander von Humboldt," Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Paulo Manrique
- Instituto de Medicina Tropical "Alexander von Humboldt," Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Jan E Conn
- Wadsworth Center, New York State Department of Health, Albany, New York.,Department of Biomedical Sciences, School of Public Health, University at Albany (State University of New York), Albany, New York
| | - Marta Moreno
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, San Diego, California
| | - Andres G Lescano
- Facultad de Salud Pública, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Juan F Sanchez
- Facultad de Salud Pública, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Hugo Rodriguez
- Dirección Regional de Salud Loreto, Ministerio de Salud, Iquitos, Peru
| | - Hermann Silva
- Dirección Regional de Salud Loreto, Ministerio de Salud, Iquitos, Peru
| | - Alejandro Llanos-Cuentas
- Instituto de Medicina Tropical "Alexander von Humboldt," Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Joseph M Vinetz
- Instituto de Medicina Tropical "Alexander von Humboldt," Universidad Peruana Cayetano Heredia, Lima, Peru.,Departamento de Ciencias Celulares y Moleculares, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru.,Division of Infectious Diseases, Department of Medicine, University of California San Diego, San Diego, California
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42
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Venkatesh A, Patel SK, Ray S, Shastri J, Chatterjee G, Kochar SK, Patankar S, Srivastava S. Proteomics ofPlasmodium vivaxmalaria: new insights, progress and potential. Expert Rev Proteomics 2016; 13:771-82. [DOI: 10.1080/14789450.2016.1210515] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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